- cache - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
- CACHE_LARGEST_OBJECT - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- CacheHoldingArrayList<E> - Class in org.intermine.util
-
This is an extension of the the ArrayList class, designed to be used by systems that return
Lists of data, with extra data that should not be flushed out of a cache until the List is
garbage collected.
- CacheHoldingArrayList() - Constructor for class org.intermine.util.CacheHoldingArrayList
-
Empty constructor
- CacheHoldingArrayList(Collection<E>) - Constructor for class org.intermine.util.CacheHoldingArrayList
-
Constructs a new instance from another Collection.
- CacheHoldingArrayList(int) - Constructor for class org.intermine.util.CacheHoldingArrayList
-
Constructs a new instance with the given initial capacity.
- cacheLines - Variable in class org.intermine.sql.precompute.OptimiserCache
-
A Map that holds a mapping from unoptimised query string (with LIMIT and OFFSET stripped off)
to a Set of OptimiserCacheLine objects.
- cacheLinks(MultiKey, Collection<PartnerLink>) - Method in class org.intermine.api.mines.FriendlyMineManager
-
- CacheMap<K,V> - Class in org.intermine.util
-
This is a Map implementation designed specifically for people intending to create a cache.
- CacheMap(int, float) - Constructor for class org.intermine.util.CacheMap
-
Constructs a new, empty CacheMap with the given initial
capacity and the given load factor.
- CacheMap(int) - Constructor for class org.intermine.util.CacheMap
-
Constructs a new, empty CacheMap with the given initial
capacity and the default load factor, which is 0.75.
- CacheMap() - Constructor for class org.intermine.util.CacheMap
-
Constructs a new, empty CacheMap with the default initial
capacity (16) and the default load factor (0.75).
- CacheMap(String) - Constructor for class org.intermine.util.CacheMap
-
Constructs a new, empty CacheMap with the default initial
capacity (16) and the default load factor (0.75), and a name.
- CacheMap(Map<K, V>) - Constructor for class org.intermine.util.CacheMap
-
Constructs a new CacheMap with the same mappings as the
specified Map.
- cacheMisses - Variable in class org.intermine.dataloader.BatchingFetcher
-
- cacheObjectById(Integer, InterMineObject) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Places an entry into the objectstore getObjectById cache.
- cacheObjectById(Integer, InterMineObject) - Method in interface org.intermine.objectstore.ObjectStore
-
Places an entry into the objectstore getObjectById cache.
- cacheObjectById(Integer, InterMineObject) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Places an entry into the objectstore getObjectById cache.
- cacheObjectById(Integer, InterMineObject) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Places an entry into the objectstore getObjectById cache.
- calculate(EnrichmentInput, Double, String, boolean, CorrectionCoefficient) - Static method in class org.intermine.web.logic.widget.EnrichmentCalculation
-
Perform an enrichment calculation based on input from some source and return results that
include a p-value and count for each attribute that was observed in the sample.
- CalculateLocations - Class in org.intermine.bio.postprocess
-
Calculate additional mappings between annotation after loading into genomic ObjectStore.
- CalculateLocations(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.CalculateLocations
-
Create a new CalculateLocations object from an ObjectStoreWriter
- CalculateLocations.SimpleLoc - Class in org.intermine.bio.postprocess
-
Lightweight representation of a Location for easier manipulation and
storing in maps.
- CalculateLocations.SimpleLoc(int, int, int, int, String) - Constructor for class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
-
Construct with integer values
- CalculateLocations.SimpleLoc(int, int, Location) - Constructor for class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
-
Construct with integer values for object and subject and a Location object
- call(Either<A, B>) - Method in class org.intermine.webservice.server.core.EitherVisitor
-
- call(A) - Method in class org.intermine.webservice.server.core.F
-
The body of the function
- call(X) - Method in class org.intermine.webservice.server.core.F.Constant
-
Call this function, returning the value supplied to the constructor.
- call(A) - Method in interface org.intermine.webservice.server.core.Function
-
Take an A and return a B.
- call(T) - Method in interface org.intermine.webservice.server.core.Predicate
-
Apply some test to some kind of thing.
- call(String) - Method in class org.intermine.webservice.server.core.RateLimitHistory
-
- Callback - Class in org.intermine.web.struts.oauth2
-
The controller that handles the requests made after the user has visited their
authorisation provider to log-in.
- Callback() - Constructor for class org.intermine.web.struts.oauth2.Callback
-
- CALLBACK_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
-
The callback to be supplied for jsonp calls
- canAssignObjectToType(Class<?>, InterMineObject) - Static method in class org.intermine.api.util.PathUtil
-
Return true if given type (of a constraint) can be assigned to the InterMineObject - i.e.
- cancelRequest(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
This method cancels any Statement running in a given request ID, and blacklists that ID.
- candidates - Variable in class org.intermine.sql.precompute.BestQueryExplainer
-
- candidateTables - Variable in class org.intermine.sql.precompute.BestQueryExplainer
-
- canDoPkNow(PrimaryKey, ClassDescriptor, Map<PrimaryKey, ClassDescriptor>) - Method in class org.intermine.dataloader.BatchingFetcher
-
Returns whether this primary key can be fetched now.
- canExport(List<Class<?>>) - Method in interface org.intermine.web.logic.export.Exporter
-
This method finds out if result row composed from instances of these
classes can be exported with actual implementation of exporter.
- canExport(List<Class<?>>) - Method in class org.intermine.web.logic.export.ExporterImpl
-
This method finds out if result row composed from instances of these
classes can be exported with actual implementation of exporter.
- canExport(PagedTable, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper
-
Return true if the specified class or a subclass is found in a column of the
paged table (or is the parent class of a field displayed in the table).
- canExport(PagedTable) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
-
- canExport(PagedTable) - Method in interface org.intermine.web.logic.export.http.TableHttpExporter
-
Check if this TableExporter can export the given PagedTable.
- canHaveCollection(String) - Method in class org.intermine.xml.full.Item
-
Return true if and only if the argument names a possible collection for this Item.
- canHaveReference(String) - Method in class org.intermine.xml.full.Item
-
Return true if and only if the argument names a possible reference for this Item.
- canonicaliseIndexes(Collection<String>) - Static method in class org.intermine.sql.precompute.PrecomputedTableManager
-
Takes a collection of index strings, and removes redundant entries.
- canServe(Format) - Method in class org.intermine.webservice.server.lists.AvailableListsService
-
- canServe(Format) - Method in class org.intermine.webservice.server.lists.ListMakerService
-
- canServe(Format) - Method in class org.intermine.webservice.server.model.ModelService
-
- canServe(Format) - Method in class org.intermine.webservice.server.path.PossibleValuesService
-
- canServe(Format) - Method in class org.intermine.webservice.server.query.CodeService
-
- canServe(Format) - Method in class org.intermine.webservice.server.query.QueryRemovalService
-
- canServe(Format) - Method in class org.intermine.webservice.server.query.QueryRetrieverService
-
- canServe(Format) - Method in class org.intermine.webservice.server.query.QueryToListService
-
- canServe(Format) - Method in class org.intermine.webservice.server.query.QueryUploadService
-
- canServe(Format) - Method in class org.intermine.webservice.server.query.result.QueryResultService
-
- canServe(Format) - Method in class org.intermine.webservice.server.query.result.TableRowService
-
- canServe(Format) - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService
-
- canServe(Format) - Method in class org.intermine.webservice.server.template.AvailableTemplatesService
-
- canServe(Format) - Method in class org.intermine.webservice.server.template.SingleTemplateService
-
- canServe(Format) - Method in class org.intermine.webservice.server.template.TemplateRemovalService
-
- canServe(Format) - Method in class org.intermine.webservice.server.template.TemplateUploadService
-
- canServe(Format) - Method in class org.intermine.webservice.server.VersionService
-
- canServe(Format) - Method in class org.intermine.webservice.server.WebService
-
Check whether the format is acceptable.
- canServe(Format) - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
-
- castBagsToCommonType(Collection<InterMineBag>, String, Set<String>, Profile, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
-
Given a common type, return a collection of bags cast to that type.
- CATEGORIES - Static variable in class org.intermine.web.logic.Constants
-
ServletContext attribute, List of category names.
- categoriseBasedOnTags(FieldDescriptor, String, DisplayField, Map<String, DisplayField>, TagManager, String, Map<String, Map<String, DisplayField>>, boolean) - Static method in class org.intermine.web.struts.ReportController
-
For a given FieldDescriptor, look up its 'aspect:' tags and place it in
the correct map within placementRefsAndCollections.
- category - Variable in class org.intermine.sql.precompute.PrecomputedTable
-
- caughtError - Variable in class org.intermine.bio.dataconversion.IdResolverFactory
-
- CEIL - Static variable in class org.intermine.objectstore.query.QueryFunction
-
Smallest integer value greater than input.
- ChadoCV - Class in org.intermine.bio.chado
-
Objects of this class represent a controlled vocabulary from chado.
- ChadoCV(String) - Constructor for class org.intermine.bio.chado.ChadoCV
-
Create a new ChadoCV.
- ChadoCVFactory - Class in org.intermine.bio.chado
-
A factory for ChadoCV objects.
- ChadoCVFactory(Connection) - Constructor for class org.intermine.bio.chado.ChadoCVFactory
-
Create a new ChadoCVFactory.
- ChadoCVTerm - Class in org.intermine.bio.chado
-
Objects of this class represent one row of the chado cvterm table.
- ChadoCVTerm(String) - Constructor for class org.intermine.bio.chado.ChadoCVTerm
-
Create a new cv term object
- ChadoDBConverter - Class in org.intermine.bio.dataconversion
-
DataConverter to read from a Chado database into items
- ChadoDBConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.bio.dataconversion.ChadoDBConverter
-
Create a new ChadoDBConverter object.
- ChadoProcessor - Class in org.intermine.bio.dataconversion
-
A processor for a chado module.
- ChadoProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.ChadoProcessor
-
Create a new ChadoModuleProcessor object.
- ChangeEvent - Interface in org.intermine.api.search
-
Events that represent changes in something.
- ChangePasswordAction - Class in org.intermine.web.struts
-
- ChangePasswordAction() - Constructor for class org.intermine.web.struts.ChangePasswordAction
-
- ChangePasswordForm - Class in org.intermine.web.struts
-
Form bean to represent the inputs needed to change a password from user input.
- ChangePasswordForm() - Constructor for class org.intermine.web.struts.ChangePasswordForm
-
- changePasswordWithToken(String, String) - Method in class org.intermine.api.profile.ProfileManager
-
Changes the password of a profile if the given token is valid.
- changePath(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
-
Change the currently active metadata Node
- changeSequence(Set<Object>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Increments the sequence numbers for the given set of database components.
- ChangeTableAction - Class in org.intermine.web.struts
-
Implementation of DispatchAction.
- ChangeTableAction() - Constructor for class org.intermine.web.struts.ChangeTableAction
-
- ChangeTableSizeAction - Class in org.intermine.web.struts
-
Changes the size of the results displayed.
- ChangeTableSizeAction() - Constructor for class org.intermine.web.struts.ChangeTableSizeAction
-
- ChangeTableSizeForm - Class in org.intermine.web.struts
-
Form bean for changing the page size.
- ChangeTableSizeForm() - Constructor for class org.intermine.web.struts.ChangeTableSizeForm
-
Constructor
- changeViewPathDescription(String, String) - Method in class org.intermine.dwr.AjaxServices
-
Set the description of a view path.
- characters(char[], int, int) - Method in class org.intermine.api.bag.BagQueryHandler
- characters(char[], int, int) - Method in class org.intermine.api.bag.InvitationHandler
- characters(char[], int, int) - Method in class org.intermine.api.profile.PreferencesHandler
- characters(char[], int, int) - Method in class org.intermine.pathquery.PathQueryHandler
- characters(char[], int, int) - Method in class org.intermine.webservice.server.ServiceListingHandler
-
- charAt(int) - Method in class org.intermine.bio.util.ClobAccessReverseComplement
-
Return a character from the specified index.
- charAt(int) - Method in class org.intermine.objectstore.query.ClobAccess
-
Return a character from the specified index.
- charAt(int) - Method in class org.intermine.objectstore.query.PendingClob
-
Return a character from the specified index.
- check(Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.precompute.OptimiserMappingChecker
-
Checks a partial mapping.
- check(Map<T, T>) - Method in interface org.intermine.util.MappingUtilChecker
-
Checks a partial mapping.
- checkAttribute(String) - Method in class org.intermine.xml.full.Item
-
Return true if the name parameter is an attribute of the class for this Item or if
the Model or the className of this Item haven't been set.
- checkCollection(String) - Method in class org.intermine.xml.full.Item
-
Throw a RuntimeException if the name parameter isn't an collection in the class set by
setClassName() in the Model set by setModel().
- checkComparisonEquals(int) - Static method in class org.intermine.sql.query.AbstractConstraint
-
Take an integer as if it was created by compare, and return true if this implies that the
left constraint is EQUAL to the right constraint, in a loose sense.
- checkComparisonImplies(int) - Static method in class org.intermine.sql.query.AbstractConstraint
-
Take an integer as if it was created by compare, and return true if this implies that the
left constraint IMPLIES the right constraint, in a loose sense.
- checkFieldExists(Model, String, String, String) - Static method in class org.intermine.bio.postprocess.PostProcessUtil
-
Check that a class exists and has a field of the given name.
- CheckForIsNotNullConstraint - Class in org.intermine.objectstore.intermine
-
For use with ConstraintHelper.traverseConstraints().
- CheckForIsNotNullConstraint(QueryNode) - Constructor for class org.intermine.objectstore.intermine.CheckForIsNotNullConstraint
-
Construct with the QueryNode to test for NOT NULL constraint.
- checkImplementations(String) - Method in class org.intermine.xml.full.Item
-
Throw RuntimeException if the given implementations don't match the model.
- checkLists(Map<String, InterMineBag>, List<String>) - Method in class org.intermine.webservice.server.lists.ListInput
-
Make sure that any lists names exist.
- checkPassword(String, String) - Static method in class org.intermine.util.PasswordHasher
-
Checks to see if a password matches an optionally hashed password entry.
- checkPathFormat(String) - Static method in class org.intermine.pathquery.PathQuery
-
Verifies the format of a path for a query.
- checkReference(String) - Method in class org.intermine.xml.full.Item
-
Throw a RuntimeException if the name parameter isn't an reference in the class set by
setClassName() in the Model set by setModel().
- checkResponse() - Method in class org.intermine.webservice.client.util.HttpConnection
-
Called to check the response and generate an appropriate exception (on failure).
- checkSequence(Map<Object, Integer>, Query, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Checks a number against the sequence number, and throws an exception if they do not match.
- checkSequence(Map<Object, Integer>, Query, String) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Checks a number against the sequence number, and throws an exception if they do not match.
- checkStartLimit(int, int, Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Checks the start and limit to see whether they are inside the
hard limits for this ObjectStore
- checkTaxonId(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
-
Check that the given taxon id has some data for it. if an exception thrown, there must be
something wrong with resolver factory.
- ChromosomeLocationHelper - Class in org.intermine.bio.query.range
-
Method to help querying for ranges
- ChromosomeLocationHelper() - Constructor for class org.intermine.bio.query.range.ChromosomeLocationHelper
-
Method to set up chromosome fields for helping
- CLASS - Static variable in class org.intermine.api.tag.TagTypes
-
A Class/ClassDescriptor.
- CLASS_KEYS - Static variable in class org.intermine.modelproduction.MetadataManager
-
The name of the key to use to store the class_keys.properties file.
- ClassChooserController - Class in org.intermine.web.struts
-
Gets list of help text blurbs for each class, and passes them on to the display page.
- ClassChooserController() - Constructor for class org.intermine.web.struts.ClassChooserController
-
- ClassConstraint - Class in org.intermine.objectstore.query
-
Constrain whether a QueryClass is equal/not equal to another
QueryClass or an example of an object belonging to a
QueryClass.
- ClassConstraint(QueryClass, ConstraintOp, QueryClass) - Constructor for class org.intermine.objectstore.query.ClassConstraint
-
Construct ClassConstraint
- ClassConstraint(QueryClass, ConstraintOp, InterMineObject) - Constructor for class org.intermine.objectstore.query.ClassConstraint
-
Construct ClassConstraint
- classConstraintToString(SqlGenerator.State, StringBuffer, ClassConstraint, Query, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Converts a ClassConstraint object into a String suitable for putting in an SQL query.
- ClassKeyHelper - Class in org.intermine.api.config
-
Methods to read and manage keys for classes.
- classKeys - Variable in class org.intermine.api.InterMineAPI
-
- ClassKeys - Interface in org.intermine.api.types
-
Type alias for classkeys - simplifies matters and prevents mistakes.
- ClassKeyServlet - Class in org.intermine.webservice.server
-
A Servlet for routing requests to the ClassKeyService.
- ClassKeyServlet() - Constructor for class org.intermine.webservice.server.ClassKeyServlet
-
- ClassKeysNotFoundException - Exception in org.intermine.api.bag
-
Exception thrown when given attempting to create a bag for a type that isn't in the model, this
can happen when reading bags from a userprofile database and the data model has changed.
- ClassKeysNotFoundException(String) - Constructor for exception org.intermine.api.bag.ClassKeysNotFoundException
-
Constructs an IncompatibleBagTypesException with the specified detail message.
- ClassKeysNotFoundException(Throwable) - Constructor for exception org.intermine.api.bag.ClassKeysNotFoundException
-
Constructs an IncompatibleBagTypesException with the specified nested throwable.
- ClassKeysNotFoundException(String, Throwable) - Constructor for exception org.intermine.api.bag.ClassKeysNotFoundException
-
Constructs an IncompatibleBagTypesException with the specified detail message and nested
throwable.
- ClassKeysService - Class in org.intermine.webservice.server
-
A service to fetch a JSON representation of class keys for all classes in the model.
- ClassKeysService(InterMineAPI) - Constructor for class org.intermine.webservice.server.ClassKeysService
-
Construct with the InterMineAPI.
- className - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput
-
- className - Variable in class org.intermine.web.struts.QueryClassSelectForm
-
- classNotExists(Class<? extends FastPathObject>) - Method in class org.intermine.dataloader.EquivalentObjectHints
-
Returns true if there were no instances of the given class in the database.
- ClassResourceOpener - Class in org.intermine.web.logic
-
Objects that open resources relative to a classpath.
- ClassResourceOpener(Class<?>) - Constructor for class org.intermine.web.logic.ClassResourceOpener
-
Constructor.
- classToType(Class<?>) - Static method in class org.intermine.objectstore.query.UnknownTypeValue
-
Converts a Class into an approximate type.
- clean() - Method in class org.intermine.dataloader.ObjectDescription
-
Marks the ObjectDescription as clean - that is all the data has been flushed to the backing
database.
- cleanTags(TagManager) - Static method in class org.intermine.web.struts.InitialiserPlugin
-
Remove class tags from the user profile that refer to classes that non longer exist
- cleanUp() - Method in class org.intermine.webservice.server.WebService
-
Subclasses may put clean-up code here, to be run after the request has
been executed.
- clear() - Method in class org.intermine.api.profile.UserPreferences
-
- clear() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Remove all items held locally in handler.
- clear() - Method in class org.intermine.dataloader.DataTracker
-
Clears the data tracker of all entries.
- clear() - Method in class org.intermine.sql.writebatch.Batch
-
Clears the batch without writing it to the database.
- clear() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
-
Clears the batch.
- clear() - Method in interface org.intermine.sql.writebatch.Table
-
Clears the batch.
- clear() - Method in class org.intermine.sql.writebatch.TableBatch
-
Clears the batch.
- clear() - Method in class org.intermine.util.AlwaysMap
- clear() - Method in class org.intermine.util.IdentityMap
- clear() - Method in class org.intermine.util.IntPresentSet
-
Removes all ints from the object.
- clear() - Method in class org.intermine.util.IntToIntMap
-
Removes all mappings from the object.
- clear() - Method in class org.intermine.util.PseudoSet
- clear() - Method in class org.intermine.util.ReferenceMap
- clear() - Method in class org.intermine.webservice.client.results.ResultRowList
-
- clearCache() - Method in class org.intermine.webservice.client.core.Service
-
Clear the cache on this object.
- clearCache() - Method in class org.intermine.webservice.client.services.ModelService
-
- clearConstraints() - Method in class org.intermine.pathquery.PathQuery
-
Clears the entire set of constraints from this query, and resets the constraint logic.
- clearConstraints() - Method in class org.intermine.template.TemplateQuery
-
Clears the entire set of constraints from this query, and resets the constraint logic.
- clearDataSetReferenceList() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Reset the list of DataSet items.
- clearDescriptions() - Method in class org.intermine.pathquery.PathQuery
-
Removes all path descriptions from this query.
- clearFinalItems() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Clear the list of final items.
- clearLocation() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Clear the location item for this record.
- clearObj(Integer) - Method in class org.intermine.dataloader.DataTracker
-
Clears the cache for a particular object, in preparation for writing all the data for that
object.
- clearOrderBy() - Method in class org.intermine.objectstore.query.Query
-
Clears the ORDER BY clause of this Query
- clearOrderBy() - Method in class org.intermine.pathquery.PathQuery
-
Clears the entire order by list.
- clearOuterJoinStatus() - Method in class org.intermine.pathquery.PathQuery
-
Clears all outer join status data from this query.
- clearProblem() - Method in class org.intermine.sql.writebatch.Batch
-
Clears the problem with the Batch.
- clearPublicationReferenceList() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Reset the list of Publication items.
- clearSelect() - Method in class org.intermine.objectstore.query.Query
-
Clears the SELECT list
- clearSelectIds() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Clear the table selection
- clearView() - Method in class org.intermine.pathquery.PathQuery
-
Clears the entire view list.
- Clob - Class in org.intermine.objectstore.query
-
Object representing a large String that has been stored in the database.
- Clob(int) - Constructor for class org.intermine.objectstore.query.Clob
-
Constructs a new Clob.
- clob - Variable in class org.intermine.objectstore.query.ClobAccess
-
- CLOB_PAGE_SIZE - Static variable in class org.intermine.objectstore.query.Clob
-
Page size for clob data
- CLOB_TABLE_NAME - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
The name of the table that stores Clobs.
- ClobAccess - Class in org.intermine.objectstore.query
-
Class used to read a Clob from the ObjectStore.
- ClobAccess() - Constructor for class org.intermine.objectstore.query.ClobAccess
-
Protected constructor for use by PendingClob only.
- ClobAccess(ObjectStore, Clob) - Constructor for class org.intermine.objectstore.query.ClobAccess
-
Construct a ClobAccess object from an ObjectStore and a Clob.
- ClobAccess.ClobAccessSubclassFactory - Class in org.intermine.objectstore.query
-
Class to provide fast access to the constructor of plugin subclasses of ClobAccess.
- ClobAccess.ClobAccessSubclassFactory() - Constructor for class org.intermine.objectstore.query.ClobAccess.ClobAccessSubclassFactory
-
- ClobAccessReverseComplement - Class in org.intermine.bio.util
-
Subclass of ClobAccess that reverses and complements the DNA sequence contained within it.
- ClobAccessReverseComplement(ClobAccess) - Constructor for class org.intermine.bio.util.ClobAccessReverseComplement
-
Construct this object from an existing ClobAccess object
- CLOBID_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
The name of the clobid column in the clob table.
- CLOBPAGE_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
The name of the page number column in the clob table.
- CLOBVAL_COLUMN - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
The name of the value column in the clob table.
- clone() - Method in class org.intermine.api.profile.InterMineBag
-
Create copy of bag.
- clone() - Method in class org.intermine.api.template.ApiTemplate
-
Clone this ApiQuery
- clone() - Method in class org.intermine.pathquery.PathQuery
-
Returns a deep copy of this object.
- clone() - Method in class org.intermine.template.TemplateQuery
-
Clone this TemplateQuery.
- cloneAttributeDescriptors(Set<AttributeDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
-
Clone a set of AttributeDescriptors.
- cloneClassDescriptor(ClassDescriptor) - Static method in class org.intermine.modelproduction.ModelMerger
-
Construct a ClassDescriptor that takes on all the properties of cld
without attaching to a particular Model.
- cloneCollectionDescriptors(Set<CollectionDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
-
Clone a set of CollectionDescriptors.
- cloneInterMineObject(O) - Static method in class org.intermine.bio.postprocess.PostProcessUtil
-
Create a clone of given InterMineObject including the id.
- cloneQuery(Query) - Static method in class org.intermine.objectstore.query.QueryCloner
-
Clones a query object.
- cloneReferenceDescriptors(Set<ReferenceDescriptor>) - Static method in class org.intermine.modelproduction.ModelMerger
-
Clone a set of ReferenceDescriptors.
- cloneWithoutEditableConstraints() - Method in class org.intermine.template.TemplateQuery
-
Return a clone of this template query with all editable constraints
removed - i.e. a query that will return all possible results of executing
the template.
- close() - Method in class org.intermine.api.bag.BagManager
-
Close the TagManager
- close() - Static method in class org.intermine.api.lucene.KeywordSearch
-
set all the variables to NULL
- close() - Method in class org.intermine.api.profile.ProfileManager
-
Close this ProfileManager
- close() - Method in class org.intermine.api.profile.TagManager
-
Close this TagManager.
- close() - Method in class org.intermine.api.tracker.TrackerDelegate
-
Release the db connection when done.
- close() - Method in class org.intermine.bio.dataconversion.BioGridConverter
-
Perform any necessary clean-up after processing
- close() - Method in class org.intermine.bio.dataconversion.GFF3Converter
-
Perform any necessary clean-up after post-conversion
- close() - Method in class org.intermine.bio.dataconversion.KeggPathwayConverter
-
Perform any necessary clean-up after processing
- close() - Method in class org.intermine.dataconversion.DataConverter
-
Perform any necessary clean-up after processing
- close() - Method in class org.intermine.dataconversion.DirectoryConverter
-
Perform any necessary clean-up after post-conversion
- close() - Method in interface org.intermine.dataconversion.ItemWriter
-
Flushes any store queue, closes transactions, and generally makes sure that every Item passed
to the store() method is committed to the destination.
- close() - Method in class org.intermine.dataconversion.MockItemWriter
-
Flushes any store queue, closes transactions, and generally makes sure that every Item passed
to the store() method is committed to the destination.
- close() - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
-
Flushes any store queue, closes transactions, and generally makes sure that every Item passed
to the store() method is committed to the destination.
- close(Source) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
-
Close method - prints out summary data.
- close(Source) - Method in class org.intermine.dataloader.BatchingFetcher
-
Close method - prints out summary data.
- close() - Method in class org.intermine.dataloader.DataTracker
-
Closes this DataTracker, releasing both connections to the database.
- close() - Method in class org.intermine.dataloader.DirectDataLoader
-
Close the DirectDataLoader, must be called to make sure final batch of data is stored.
- close(Source) - Method in class org.intermine.dataloader.HintingFetcher
-
Close method - prints out summary data.
- close() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Closes the connection associated with this ObjectStoreWriter
- close() - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
-
Closes the connection associated with this ObjectStoreWriter
- close(Source) - Method in class org.intermine.dataloader.ParallelBatchingFetcher
-
Close method - prints out summary data.
- close() - Method in class org.intermine.dataloader.XmlDataLoader
-
Perform any necessary clean-up and close the integration writer
- close() - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectInputStream
-
- close() - Method in class org.intermine.modelproduction.MetadataManager.LargeObjectOutputStream
-
- close() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Closes this ObjectStore's DB log connection.
- close() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Closes this ObjectStore's DB log connection.
- close() - Method in interface org.intermine.objectstore.ObjectStoreWriter
-
Closes the connection associated with this ObjectStoreWriter
- close() - Method in class org.intermine.sql.logging.DatabaseWriter
-
Close this Writer
- close(Connection) - Method in class org.intermine.sql.writebatch.Batch
-
Closes this BatchWriter.
- close() - Method in class org.intermine.webservice.client.util.HttpConnection
-
Closes connection.
- closeIndexWriter() - Method in class org.intermine.web.autocompletion.LuceneIndex
-
close the current indexWriter
- closeSituation - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
- cls - Variable in class org.intermine.objectstore.query.ContainsConstraint
-
- cls - Variable in class org.intermine.objectstore.query.SubqueryConstraint
-
- clsCol - Variable in class org.intermine.bio.dataconversion.IdResolverFactory
-
- clsName - Variable in class org.intermine.task.AnalyseDbTask
-
- clsName - Variable in class org.intermine.task.DirectoryConverterTask
-
- clsName - Variable in class org.intermine.task.FileConverterTask
-
- clsName - Variable in class org.intermine.task.PostProcessorTask
-
- COALESCE - Static variable in class org.intermine.sql.query.Function
-
COALESCE operator - used by the precomputed tables' orderby fields.
- CodeService - Class in org.intermine.webservice.server.query
-
A service for generating code based on a query.
- CodeService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.CodeService
-
Constructor.
- CodeServlet - Class in org.intermine.webservice.server.query
-
A servlet for routing requests to the code service.
- CodeServlet() - Constructor for class org.intermine.webservice.server.query.CodeServlet
-
- CodeTranslator - Class in org.intermine.webservice.server
-
Translates strings between codes used in ConstraintOp class and abbreviations or
full code names of operations.
- collapse(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeAction
-
Process the specified HTTP request, and create the corresponding HTTP
response (or forward to another web component that will create it).
- COLLECTION - Static variable in class org.intermine.api.tag.TagTypes
-
Collection.
- CollectionDetailsAction - Class in org.intermine.web.struts
-
Action that creates a table of collection elements for display.
- CollectionDetailsAction() - Constructor for class org.intermine.web.struts.CollectionDetailsAction
-
- CollectionTableAction - Class in org.intermine.web.struts
-
Action that creates a table of collection elements for display in a table widget.
- CollectionTableAction() - Constructor for class org.intermine.web.struts.CollectionTableAction
-
- collectionToSQLString(Collection<? extends SQLStringable>, String) - Static method in class org.intermine.sql.query.Query
-
Converts a collection of objects that implement the getSQLString method into a String,
with the given comma string between each element.
- collectionToSQLString(Collection<? extends SQLStringable>, Collection<String>, String) - Static method in class org.intermine.sql.query.Query
-
Converts a collection of objects that implement the getSQLString method into a String,
with the given comma string between each element.
- CollectionUtil - Class in org.intermine.util
-
Utilities for Collections.
- Column - Class in org.intermine.api.results
-
Configuration information for a column in a table
- Column(Path, String, int, Class) - Constructor for class org.intermine.api.results.Column
-
Constructor that takes a Path object.
- Column(Path, int, Class) - Constructor for class org.intermine.api.results.Column
-
Constructor that takes a Path object.
- Column(String, int, Class) - Constructor for class org.intermine.api.results.Column
-
Constructor that takes a String name.
- COLUMN_HEADERS - Static variable in class org.intermine.webservice.server.output.FlatFileFormatter
-
The key for the header columns
- columnExists(Connection, String, String) - Static method in class org.intermine.sql.DatabaseUtil
-
Tests if a column exists in the database
- columnFullNames - Variable in class org.intermine.web.logic.results.InlineResultsTable
-
- ColumnHeaderStyle - Enum in org.intermine.webservice.server
-
Enumeration for outer join status.
- columnId - Variable in class org.intermine.api.results.Column
-
- combineBags() - Method in class org.intermine.api.bag.operations.BagOperation
-
- combineBags() - Method in class org.intermine.api.bag.operations.RelativeComplement
-
- CombinedIterator<E> - Class in org.intermine.util
-
An Iterator that combines the contents of various other Iterators.
- CombinedIterator(List<Iterator<? extends E>>) - Constructor for class org.intermine.util.CombinedIterator
-
Constructs a CombinedIterator from a List of Iterators.
- combineWith(ProfileMergeIssues) - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
-
Combine this set of merge issues with another set.
- comment - Variable in class org.intermine.template.TemplateQuery
-
The private comment for this query.
- commitTransaction() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Request that the ObjectStore commits and closes the transaction, delegate to internal
ObjectStoreWriter.
- commitTransaction() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Request that the ObjectStoreWriter commits and closes the transaction
- commitTransaction() - Method in interface org.intermine.objectstore.ObjectStoreWriter
-
Request that the ObjectStoreWriter commits and closes the transaction
- commitTransactionWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Commits a transaction.
- COMMON_KEYS - Static variable in class org.intermine.api.profile.UserPreferences
-
Common keys
- CommutativeOperationInput - Class in org.intermine.webservice.server.lists
-
An input class for operations that are commutative.
- CommutativeOperationInput(HttpServletRequest, BagManager, Profile) - Constructor for class org.intermine.webservice.server.lists.CommutativeOperationInput
-
Constructor.
- comparable(Class<?>, Class<?>) - Static method in class org.intermine.objectstore.query.SimpleConstraint
-
Check whether the two arguments are of comparable types i.e. they are of similiar type
and we know how to handle that type
- compare(String, String) - Method in class org.intermine.api.bag.BagManager.ByTagOrder
-
- compare(String, String) - Method in class org.intermine.api.bag.BagManager.CaseInsensitiveComparator
-
- compare(InterMineObject, InterMineObject) - Method in class org.intermine.dataloader.SourcePriorityComparator
-
Compares two objects.
- compare(Path, Path) - Method in class org.intermine.pathquery.PathLengthComparator
-
Compare paths by number elements they contain, shortest paths come first.
- compare(AbstractTable, AbstractTable) - Method in class org.intermine.sql.precompute.QueryOptimiser.AbstractTableComparator
-
Compare two AbstractTables using equalsIgnoreAlias().
- compare(AbstractConstraint) - Method in class org.intermine.sql.query.AbstractConstraint
-
Compare this AbstractConstraint with another, ignoring aliases in member fields and tables.
- compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractConstraint
-
Compare this AbstractConstraint with another, ignoring aliases in member fields and tables.
- compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
-
Compare the value of this AbstractValue with another.
- compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Constant
-
Compare this Constant to another AbstractValue.
- compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Constraint
-
Compare this Constraint with another AbstractConstraint, ignoring aliases in member fields
and tables.
- compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.ConstraintSet
-
Compare this ConstraintSet with another AbstractConstraint, ignoring aliases in member
fields and tables.
- compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Field
-
Compare this field to another AbstractValue.
- compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.Function
-
Compare the value of this AbstractValue with another.
- compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.InListConstraint
-
Compare this InListConstraint with another AbstractConstraint, ignoring aliases in member
fields and tables.
- compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.NotConstraint
-
Compare this NotConstraint with another AbstractConstraint, ignoring aliases in member
fields and tables.
- compare(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.OrderDescending
-
Compare the value of this AbstractValue with another.
- compare(AbstractConstraint, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.SubQueryConstraint
-
Compare this SubQueryConstraint with another AbstractConstraint, ignoring aliases in member
fields and tables.
- compare(TemplateQuery, TemplateQuery) - Method in class org.intermine.template.TemplateComparator
-
Compare two TemplateQuery objects by title, falling back to name if the titles are
identical.
- compare(Object, Object) - Method in class org.intermine.util.NullFirstComparator
- compare(Object, Object) - Method in class org.intermine.xml.full.RendererComparator
-
Compare two Class objects by name.
- compareConstraints(Set<AbstractConstraint>, Set<AbstractConstraint>, Set<AbstractConstraint>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
-
Compares 2 sets of AbstractConstraints
- compareConstraints(Set<AbstractConstraint>, Set<AbstractConstraint>, Set<AbstractConstraint>, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
-
Compares 2 sets of AbstractConstraints
- comparesActualToExpected() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- compareSelectLists(List<SelectValue>, List<SelectValue>) - Static method in class org.intermine.sql.precompute.QueryOptimiser
-
Compares two Lists of SelectValues, and returns true if all the items in the first List are
present in the second List, ignoring the SelectValue alias.
- compareTo(ParallelPrecomputer.Job) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer.Job
- compareTo(PrecomputedTable) - Method in class org.intermine.sql.precompute.PrecomputedTable
-
Implements Comparable's method, so we can put PrecomputedTable objects into SortedMaps.
- compareTo(Row) - Method in class org.intermine.sql.writebatch.Row
- compareTo(SummaryPath) - Method in class org.intermine.web.logic.querybuilder.SummaryPath
- compareTo(Item) - Method in class org.intermine.xml.full.Item
-
Compare items first by class, then by identifier, intended for creating
ordered output files.
- complete - Variable in class org.intermine.objectstore.query.ResultsInfo
-
- complete - Variable in class org.intermine.sql.query.ExplainResult
-
- completelyFalse(Constraint) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Returns true if this constraint is always false, regardless of row values.
- CompletelyFalseException - Exception in org.intermine.objectstore.intermine
-
Exception thrown if a Constraint is deemed to be completely false.
- CompletelyFalseException() - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException
-
Constructor.
- CompletelyFalseException(String) - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException
-
Constructor.
- CompletelyFalseException(Throwable) - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException
-
Constructor.
- CompletelyFalseException(String, Throwable) - Constructor for exception org.intermine.objectstore.intermine.CompletelyFalseException
-
Constructor.
- completelyTrue(Constraint) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Returns true if this constraint is always true, regardless of row values.
- compose(F<B, C>) - Method in class org.intermine.webservice.server.core.F
-
Compose two functions f and g producing a function h such that h(x) = f(g(x)).
- composeClass(Class<?>...) - Static method in class org.intermine.util.DynamicUtil
-
Return the Class for the array of Class objects.
- composeClass(Set<Class<?>>) - Static method in class org.intermine.util.DynamicUtil
-
Return the Class for a set of Class objects.
- composeDescriptiveClass(Class<?>...) - Static method in class org.intermine.util.DynamicUtil
-
Return the Class for the array of Class objects.
- COMPUTE_TOTAL_COUNT_PARAMETER - Static variable in class org.intermine.webservice.server.query.result.QueryResultRequestParser
-
Compute total count parameter name.
- con - Variable in class org.intermine.sql.logging.DatabaseWriter
-
- con - Variable in class org.intermine.sql.precompute.BestQueryExplainer
-
- con - Variable in class org.intermine.sql.query.NotConstraint
-
- con - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
-
- config - Variable in class org.intermine.web.displayer.ReportDisplayer
-
- config - Variable in class org.intermine.web.logic.widget.Widget
-
- ConfigAction - Class in org.intermine.bio.chado.config
-
A class that represents an action while processing synonyms, dbxrefs, etc.
- ConfigAction() - Constructor for class org.intermine.bio.chado.config.ConfigAction
-
- configAttr - Variable in class org.intermine.bio.dataconversion.GFF3Converter
-
- configAttrClass - Variable in class org.intermine.bio.dataconversion.GFF3Converter
-
- configExclude - Variable in class org.intermine.bio.dataconversion.GFF3Converter
-
- configFileName - Variable in class org.intermine.task.SummariseObjectStoreTask
-
- configTerm - Variable in class org.intermine.bio.dataconversion.GFF3Converter
-
- ConfigurableMine - Interface in org.intermine.api.mines
-
A sub-interface of Mine to encapsulate the mutable elements of the interface, and not
expose them the the consumer.
- ConfigurableWebServiceServlet - Class in org.intermine.webservice.server.core
-
A servlet that can be configured entirely in XML.
- ConfigurableWebServiceServlet() - Constructor for class org.intermine.webservice.server.core.ConfigurableWebServiceServlet
-
- ConfigurationException - Exception in org.intermine.api.mines
-
An error caused when trying to configure something.
- ConfigurationException(String) - Constructor for exception org.intermine.api.mines.ConfigurationException
-
Construct an exception with a message.
- configure(Properties) - Method in interface org.intermine.api.mines.ConfigurableMine
-
Configure this mine with a the properties provided.
- configure(Properties) - Method in class org.intermine.api.mines.HttpRequester
-
- configure(Properties) - Method in class org.intermine.api.mines.LocalMine
-
- configure(Properties) - Method in interface org.intermine.api.mines.MineRequester
-
Accept configuration provided in the form of properties.
- configure(Properties) - Method in class org.intermine.api.mines.RemoteMine
-
- configure(Properties) - Method in class org.intermine.sql.Database
-
Configures a datasource from a Properties object
- configureDagTerm(Map<?, ?>) - Method in class org.intermine.bio.ontology.OboParser
-
Configure dag terms with values from one entry.
- configureDynamicAttributes(Object) - Method in class org.intermine.task.DynamicAttributeTask
-
Look at set methods on a target object and lookup values in project
properties.
- configureItem(String, Item, OboTerm) - Method in class org.intermine.bio.dataconversion.OboConverter
-
Set up attributes and references for the Item created from a DagTerm.
- configureSynonymItem(OboTermSynonym, Item, OboTerm) - Method in class org.intermine.bio.dataconversion.OboConverter
-
Set up attributes and references for the Item created from a DagTermSynonym.
- conn - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
- conn - Variable in class org.intermine.sql.precompute.PrecomputedTableManager
-
- connect() - Method in class org.intermine.webservice.client.util.HttpConnection
-
Opens connection.
- connection - Variable in class org.intermine.api.tracker.TrackerDelegate
-
- connection - Variable in class org.intermine.api.tracker.xml.TrackHandler
-
- connectionTakenBy - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
- connInUse - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
- cons - Variable in class org.intermine.sql.query.ConstraintSet
-
- ConsistentSet<E> - Class in org.intermine.util
-
A Set that allows for its member objects to be changed whilst still
belonging to the set.
- ConsistentSet() - Constructor for class org.intermine.util.ConsistentSet
-
Constructor.
- Constant - Class in org.intermine.sql.query
-
A representation of a constant value in an SQL query.
- Constant(String) - Constructor for class org.intermine.sql.query.Constant
-
Constructor for this Constant object.
- constant(B) - Static method in class org.intermine.webservice.server.core.F
-
Construct a constant function that discards its input
and always returns the same value.
- Constants - Class in org.intermine.api.config
-
A single constant.
- Constants - Class in org.intermine.bio.util
-
- Constants - Class in org.intermine.web.logic
-
Container for ServletContext and Session attribute names used by the webapp
- Constraint - Class in org.intermine.objectstore.query
-
Abstract reperesentation of a query constraint.
- Constraint() - Constructor for class org.intermine.objectstore.query.Constraint
-
- Constraint - Class in org.intermine.sql.query
-
A representation of a normal constraint, comparing two AbstractValue objects.
- Constraint(AbstractValue, int, AbstractValue) - Constructor for class org.intermine.sql.query.Constraint
-
Constructor for a Constraint object.
- constraintAttributes - Variable in class org.intermine.pathquery.PathQueryHandler
-
- constraintCode - Variable in class org.intermine.pathquery.PathQueryHandler
-
- constraintDescriptions - Variable in class org.intermine.template.TemplateQuery
-
Descriptions of constraints
- ConstraintHelper - Class in org.intermine.objectstore.query
-
Static methods to create Lists of Constraint objects in a query and
Constraints in a query relating to a given QueryClass, plus helper methods
for dealing with Constraints.
- ConstraintInput - Class in org.intermine.web.logic.template
-
Simple object that carries constraint values for other processing.
- ConstraintInput(String, String, String, ConstraintOp, String, List<String>, String) - Constructor for class org.intermine.web.logic.template.ConstraintInput
-
ConstraintLoad constructor.
- constraintLogic - Variable in class org.intermine.pathquery.PathQueryHandler
-
- ConstraintOptions - Class in org.intermine.api.query.range
-
A bundle of options consumed by the AbstractHelper when generating constraint
sets for a set of ranges.
- ConstraintOptions(ConstraintOp, ConstraintOp, ConstraintOp, ConstraintOp) - Constructor for class org.intermine.api.query.range.ConstraintOptions
-
Construct a new set of constraint options.
- ConstraintOptions(ConstraintOp, ConstraintOp, ConstraintOp, ConstraintOp, String, String) - Constructor for class org.intermine.api.query.range.ConstraintOptions
-
Construct a new set of constraint options.
- constraintPath - Variable in class org.intermine.pathquery.PathQueryHandler
-
- constraints - Variable in class org.intermine.objectstore.query.ConstraintSet
-
- Constraints - Class in org.intermine.pathquery
-
Builds constraints for the PathQuery.
- ConstraintSet - Class in org.intermine.objectstore.query
-
Groups a series of Constraints together.
- ConstraintSet(ConstraintOp) - Constructor for class org.intermine.objectstore.query.ConstraintSet
-
Construct empty ConstraintSet
- ConstraintSet - Class in org.intermine.sql.query
-
A representation of a set of constraints ORed together.
- ConstraintSet() - Constructor for class org.intermine.sql.query.ConstraintSet
-
Constructor for a ConstraintSet object.
- constraintSetToString(SqlGenerator.State, StringBuffer, ConstraintSet, Query, DatabaseSchema, int, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Converts a ConstraintSet object into a String suitable for putting in an SQL query.
- constraintSwitchOffAbility - Variable in class org.intermine.template.TemplateQuery
-
Configuration for switch-off-ability of constraints
- constraintToString(SqlGenerator.State, StringBuffer, Constraint, Query, DatabaseSchema, int, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Converts a Constraint object into a String suitable for putting in an SQL query.
- constraintToString(Query, Constraint, List<Object>) - Static method in class org.intermine.objectstore.query.iql.IqlQuery
-
Converts a Constraint into a String.
- ConstraintTraverseAction - Interface in org.intermine.objectstore.query
-
ConstraintTraverseActions are passed to the traverseConstraints() method.
- ConstraintValueParser - Class in org.intermine.pathquery
-
Parser for parsing constraint value.
- constraintValues - Variable in class org.intermine.pathquery.PathQueryHandler
-
- ConstraintWithBag - Interface in org.intermine.objectstore.query
-
Common interface for BagConstraint and MultipleInBagConstraint defining the getBag() method.
- constructQueries(boolean, ObjectStore, String, String) - Static method in class org.intermine.task.PrecomputeTask
-
Create queries for given path.
- constructQuery(Model, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
-
Construct an objectstore query represented by the given path.
- ContactAction - Class in org.intermine.web.struts
-
Action handles submission of user feedback form.
- ContactAction() - Constructor for class org.intermine.web.struts.ContactAction
-
- ContactForm - Class in org.intermine.web.struts
-
Form bean representing feedback form.
- ContactForm() - Constructor for class org.intermine.web.struts.ContactForm
-
Creates a new instance of ContactForm
- contains(String, String) - Static method in class org.intermine.pathquery.Constraints
-
Creates a constraint for a path to contain a value.
- contains(Object) - Method in class org.intermine.util.AlwaysSet
- contains(int) - Method in class org.intermine.util.IntPresentSet
-
Returns whether the given int is present in this set.
- contains(Integer) - Method in class org.intermine.util.IntPresentSet
-
Returns whether the given Integer is present in this set.
- contains(Collection<?>, Object) - Static method in class org.intermine.web.logic.WebUtil
-
So we can test set membership in JSPs.
- contains(Object) - Method in class org.intermine.webservice.client.lists.ItemList
-
- contains(Object) - Method in class org.intermine.webservice.client.results.ResultRowList
-
- contains(ItemList, Item...) - Method in class org.intermine.webservice.client.services.ListService
-
Report whether the given list contains all the items in the
supplied array.
- containsAll(Collection<?>) - Method in class org.intermine.util.AlwaysSet
- containsAll(Collection<?>) - Method in class org.intermine.util.PseudoSet
- containsAll(Collection) - Method in class org.intermine.webservice.client.lists.ItemList
-
- containsAll(Collection<?>) - Method in class org.intermine.webservice.client.results.ResultRowList
-
- containsCollections() - Method in class org.intermine.pathquery.Path
-
Return true if and only if any part of the path is a collection.
- ContainsConstraint - Class in org.intermine.objectstore.query
-
Constrain whether a QueryClass is member of a QueryReference or not.
- ContainsConstraint(QueryReference, ConstraintOp, QueryClass) - Constructor for class org.intermine.objectstore.query.ContainsConstraint
-
Constructor for ContainsConstraint.
- ContainsConstraint(QueryReference, ConstraintOp, InterMineObject) - Constructor for class org.intermine.objectstore.query.ContainsConstraint
-
Constructor for ContainsConstraint.
- ContainsConstraint(QueryReference, ConstraintOp) - Constructor for class org.intermine.objectstore.query.ContainsConstraint
-
Constructor for ContainsConstraint, constrain a reference/collection to be NULL/ NOT NULL
- containsConstraintToString(SqlGenerator.State, StringBuffer, ContainsConstraint, Query, DatabaseSchema, int, boolean) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Converts a ContainsConstraint object into a String suitable for putting in an SQL query.
- containsHeaders(String, StringBuffer) - Method in class org.intermine.web.struts.ContactForm
-
Check part of the message for injected headers.
- containsKey(Object) - Method in class org.intermine.util.AlwaysMap
- containsKey(Object) - Method in class org.intermine.util.IdentityMap
- containsKey(Object) - Method in class org.intermine.util.ReferenceMap
- containsKey(Object) - Method in class org.intermine.web.logic.results.ReportObjectFactory
-
Always returns true because get always returns an Object.
- containsKey(Map<?, ?>, Object) - Static method in class org.intermine.web.logic.WebUtil
-
So we can test map membership in JSPs.
- containsReferences() - Method in class org.intermine.pathquery.Path
-
Return true if and only if any part of the path is a reference.
- containsValue(Object) - Method in class org.intermine.util.AlwaysMap
- containsValue(Object) - Method in class org.intermine.util.IdentityMap
- containsValue(Object) - Method in class org.intermine.util.ReferenceMap
- ContentType - Enum in org.intermine.api.mines
-
An enumeration of the content-types we know about.
- ContentType - Class in org.intermine.webservice.client.core
-
Simple class wrapping content type information.
- ContextNotInitialisedException - Exception in org.intermine.web.context
-
An error thrown when the InterMineContext object has not been initialised.
- ContextNotInitialisedException(String) - Constructor for exception org.intermine.web.context.ContextNotInitialisedException
-
- convert(ResultSet, Query, ObjectStoreInterMineImpl, Connection, Map<Object, Integer>, boolean, ExtraQueryTime, Set<PrecomputedTable>, OptimiserCache) - Static method in class org.intermine.objectstore.intermine.ResultsConverter
-
Method to convert from SQL results to InterMine object-based results.
- convert(List<ResultElement>, Collection<Path>, Collection<Path>) - Method in class org.intermine.web.logic.export.ResultElementConverter
-
Converts data from ResultElement to Objects.
- convert(Item) - Static method in class org.intermine.xml.full.ItemHelper
-
Convert an XML item to a data model one
- convert(ReferenceList) - Static method in class org.intermine.xml.full.ItemHelper
-
Convert a xml ReferenceList to a fulldata ReferenceList that can then be stored with
ItemWriter
- convert(Reference) - Static method in class org.intermine.xml.full.ItemHelper
-
Convert a xml Reference to a fulldata Reference that can then be stored with
ItemWriter
- convert(Attribute) - Static method in class org.intermine.xml.full.ItemHelper
-
Convert a xml Attribute to a fulldata Attribute that can then be stored with
ItemWriter
- convert(Item) - Static method in class org.intermine.xml.full.ItemHelper
-
Convert a data model item to an XML one
- ConvertBagController - Class in org.intermine.web.struts
-
- ConvertBagController() - Constructor for class org.intermine.web.struts.ConvertBagController
-
- ConvertedObjectPair - Class in org.intermine.api.bag
-
A class to represent the mapping between an object before type conversion and the converted
object.
- ConvertedObjectPair(InterMineObject, InterMineObject) - Constructor for class org.intermine.api.bag.ConvertedObjectPair
-
Create a new ConvertedObjectPair.
- converter - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
- converter - Variable in class org.intermine.bio.task.GFF3ConverterTask
-
- ConverterTask - Class in org.intermine.task
-
Task superclass for invoking converters.
- ConverterTask() - Constructor for class org.intermine.task.ConverterTask
-
- convertToClasses(Set<String>) - Static method in class org.intermine.util.DynamicUtil
-
Convert a set of interface names to a set of Class objects
- copyField(FastPathObject, FastPathObject, Source, Source, FieldDescriptor, int) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Copies the value of the field given from the source object into the destination object.
- copyInterMineObject(O) - Static method in class org.intermine.bio.postprocess.PostProcessUtil
-
Create a copy of given InterMineObject with *no* id set and copies of collections
- correction - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
-
- CorrectionCoefficient - Interface in org.intermine.web.logic.widget
-
An Interface which defines when/how a correction coefficient can be applied
to the results obtained by a enrichment widget
- correctOfficialName(String, String) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Unify variations on similar official names.
- count(PathQuery) - Method in class org.intermine.api.query.QueryExecutor
-
Take a query and return the results row count.
- count - Variable in class org.intermine.dataconversion.FullXmlConverter
-
- count(Query, Map<Object, Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Counts the number of rows the query will produce
- count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Counts the number of rows the query will produce
- count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Counts the number of rows the query will produce
- count(Query, Map<Object, Integer>) - Method in interface org.intermine.objectstore.ObjectStore
-
Counts the number of rows the query will produce
- count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Counts the number of rows the query will produce
- COUNT - Static variable in class org.intermine.objectstore.query.QueryFunction
-
Count rows
- count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.safe.ObjectStoreSafeImpl
-
Counts the number of rows the query will produce
- count(Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
-
Counts the number of rows the query will produce
- COUNT - Static variable in class org.intermine.sql.query.Function
-
COUNT(*) aggregate function - takes no operands.
- CountProcessor - Class in org.intermine.webservice.server.core
-
A class that processes counts.
- CountProcessor() - Constructor for class org.intermine.webservice.server.core.CountProcessor
-
Constructor
- countResolutions(String, String) - Method in class org.intermine.bio.dataconversion.DoNothingIdResolver
-
- countResolutions(String, String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
-
Return the count of matching primary identifiers for a particular identifier
- countResolutions(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
-
Return the count of matching primary identifiers for a particular identifier
- CountTableController - Class in org.intermine.web.struts
-
Start a count in a separate thread of the number of rows in the PagedTable given by the
"resultsTable" request attribute.
- CountTableController() - Constructor for class org.intermine.web.struts.CountTableController
-
- countWithConnection(Connection, Query, Map<Object, Integer>) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Counts the results in a query, given a Connection.
- create() - Method in class org.intermine.bio.postprocess.CreateLocationOverlapIndex
-
Create an int4range or bioseg index on the start and end columns of the of the location
table.
- create(Class<? extends FastPathObject>, Class<?>[]) - Static method in class org.intermine.util.DynamicBean
-
Create a DynamicBean
- CREATE_SYNONYM_ACTION - Static variable in class org.intermine.bio.dataconversion.SequenceProcessor
-
An action that makes a synonym.
- CreateAccountAction - Class in org.intermine.web.struts
-
- CreateAccountAction() - Constructor for class org.intermine.web.struts.CreateAccountAction
-
- CreateAccountForm - Class in org.intermine.web.struts
-
Form bean to represent the inputs to create a new user account
- CreateAccountForm() - Constructor for class org.intermine.web.struts.CreateAccountForm
-
- createAllelesTempTable(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Create a temporary table of allele feature_ids.
- createAnonymousProfile() - Method in class org.intermine.api.profile.ProfileManager
-
Create a profile not tied to an entry in the user db.
- createAttributePath(String[], int) - Method in class org.intermine.web.logic.widget.WidgetLdr
-
Return the path of the attribute at the the position index in the paths given in input
without reference to subclass.
- createBag(String, String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.Profile
-
Create a bag and save it to the userprofile database.
- createBag(String, String, String, Map) - Method in class org.intermine.api.util.AnonProfile
-
- createBagFromPathQuery(PathQuery, String, String, String, Profile, InterMineAPI) - Static method in class org.intermine.web.logic.bag.BagHelper
-
Create a bag for the given profile and bag name from a PathQuery.
- createBagTable(Database, Connection, String, Collection<?>, Class<?>) - Static method in class org.intermine.sql.DatabaseUtil
-
Create a new table the holds the contents of the given Collection (bag).
- createBagValuesTables(Connection) - Static method in class org.intermine.sql.DatabaseUtil
-
Create the table 'bagvalues' containing the values of the key field objects
contained in a bag and an extra values
- createBasicLocalProfile(String, String, String) - Method in class org.intermine.api.profile.ProfileManager
-
Create a new Profile with the given username, password and
api-key.
- createClassFindingQuery(Model, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
-
Takes a String representation of a query (a path), and creates a query.
- createClob() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Creates a new empty Clob that is valid for this ObjectStore.
- createClob() - Method in interface org.intermine.objectstore.ObjectStore
-
Creates a new empty Clob that is valid for this ObjectStore.
- createClob() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Creates a new empty Clob that is valid for this ObjectStore.
- createClob() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Creates a new empty Clob that is valid for this ObjectStore.
- CreateCollectionAction - Class in org.intermine.bio.chado.config
-
An action that creates a collection of objects from value.
- CreateCollectionAction(String, String, String, boolean) - Constructor for class org.intermine.bio.chado.config.CreateCollectionAction
-
Create a new CreateCollectionAction object.
- createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.api.query.range.AbstractHelper
-
Extending classes may with to override this method if they need to adjust the
main constraint set in some way, such as adding an extra constraint.
- createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.api.query.range.IntHelper
-
- createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.api.query.range.StringHelper
-
- createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in interface org.intermine.api.query.RangeHelper
-
- createConstraint(Queryable, QueryNode, PathConstraintRange) - Method in class org.intermine.bio.query.range.ChromosomeLocationHelper
-
- createConstraintStructure(LogicExpression, ConstraintSet, Map<String, Constraint>) - Static method in class org.intermine.api.query.MainHelper
-
Given a LogicExpression, a Map from codes to Constraint objects, and a ConstraintSet to put
it all in, construct a tree of ConstraintSets that reflects the expression.
- createConstraintStructure(LogicExpression.Node, ConstraintSet, Map<String, Constraint>) - Static method in class org.intermine.api.query.MainHelper
-
Given a LogicExpression.Node, a Map from codes to Constraint objects, and a ConstraintSet to
put it all in, construct a tree of ConstraintSets that reflects the expression.
- createCrossReference(String, String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
-
Create a new CrossReference.
- createCrossReference(String, String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioFileConverter
-
Create a new CrossReference.
- createDefaultBagQuery(String, BagQueryConfig, Model, Map<String, List<FieldDescriptor>>, Collection<String>) - Static method in class org.intermine.api.bag.BagQueryHelper
-
Create a BagQuery that constrains the class key fields of the given type.
- createDefaultFeedbackMsg(HttpServletRequest) - Method in class org.intermine.web.struts.ContactForm
-
Create the default feedback messages.
- createFeatureTempTable(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Create a temporary table containing only the features that interest us.
- createFlankingFeatures() - Method in class org.intermine.bio.postprocess.CreateFlankingRegions
-
Iterate over genes in database and create flanking regions.
- CreateFlankingRegions - Class in org.intermine.bio.postprocess
-
Create features to represent flanking regions of configurable distance either side of gene
features.
- CreateFlankingRegions(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.CreateFlankingRegions
-
Create a new CreateFlankingRegions object that will operate on the given
ObjectStoreWriter.
- createFromDb(Set<String>, Database) - Method in class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory
-
- createFromDb(Database) - Method in class org.intermine.bio.dataconversion.IdResolverFactory
-
Read IdResolver contents from a database.
- createFromDb(String, Database) - Method in class org.intermine.bio.dataconversion.IdResolverFactory
-
Read IdResolver contents from a database.
- createFromDb(Set<String>, Database) - Method in class org.intermine.bio.dataconversion.IdResolverFactory
-
Read IdResolver contents from a database.
- createFromDb(Database) - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory
-
- createFromDb(Database) - Method in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory
-
- createFromFile(File) - Method in class org.intermine.bio.dataconversion.EnsemblIdResolverFactory
-
Populate the ID resolver from a tab delimited file
- createFromFile(File, Set<String>) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
Populate the ID resolver from a tab delimited file
- createFromFile(File) - Method in class org.intermine.bio.dataconversion.HgncIdResolverFactory
-
Populate the ID resolver from a tab delimited file
- createFromFile(File) - Method in class org.intermine.bio.dataconversion.HumanIdResolverFactory
-
Populate the ID resolver from a tab delimited file
- createFromFile(File) - Method in class org.intermine.bio.dataconversion.MgiIdentifiersResolverFactory
-
Populate the ID resolver from a tab delimited file
- createFromFile(File) - Method in class org.intermine.bio.dataconversion.RgdIdentifiersResolverFactory
-
Populate the ID resolver from a tab delimited file
- createFromFile(File) - Method in class org.intermine.bio.dataconversion.ZfinIdentifiersResolverFactory
-
Populate the ID resolver from a tab delimited file
- createFromWb2NcbiFile(File) - Method in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory
-
Populate the ID resolver from a tab delimited file
- createFromWormIdFile(File) - Method in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory
-
Populate the ID resolver from a tab delimited file
- createGetRequest(String, ContentType) - Method in class org.intermine.webservice.client.core.Service
-
Creates GET request.
- createIdResolver() - Method in class org.intermine.bio.dataconversion.DoNothingIdResolverFactory
-
- createIdResolver() - Method in class org.intermine.bio.dataconversion.EnsemblIdResolverFactory
-
- createIdResolver(String) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
Build an IdResolver from Entrez Gene gene_info file
- createIdResolver(Set<String>) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
Build an IdResolver from Entrez Gene gene_info file.
- createIdResolver() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
- createIdResolver() - Method in class org.intermine.bio.dataconversion.FlyBaseIdResolverFactory
-
Build an IdResolver for FlyBase by accessing a FlyBase chado database.
- createIdResolver() - Method in class org.intermine.bio.dataconversion.HgncIdResolverFactory
-
Build an IdResolver for HGNC.
- createIdResolver() - Method in class org.intermine.bio.dataconversion.HumanIdResolverFactory
-
- createIdResolver() - Method in class org.intermine.bio.dataconversion.IdResolverFactory
-
Create and IdResolver from source information.
- createIdResolver() - Method in class org.intermine.bio.dataconversion.MgiIdentifiersResolverFactory
-
- createIdResolver() - Method in class org.intermine.bio.dataconversion.MockIdResolverFactory
-
- createIdResolver() - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory
-
Build an IdResolver.
- createIdResolver() - Method in class org.intermine.bio.dataconversion.RgdIdentifiersResolverFactory
-
- createIdResolver() - Method in class org.intermine.bio.dataconversion.WormBaseIdResolverFactory
-
Build an IdResolver for WormBase by accessing a WormBase chado database.
- createIdResolver() - Method in class org.intermine.bio.dataconversion.ZfinIdentifiersResolverFactory
-
Build an IdResolver from Entrez Gene gene_info file
- createIndex(Connection, String, IndexStatement, int) - Method in class org.intermine.task.CreateIndexesTask
-
Create an named index on the specified columns of a table.
- CreateIndexesTask - Class in org.intermine.task
-
Task to create indexes on a database holding objects conforming to a given model by
reading that model's primary key configuration information.
- CreateIndexesTask() - Constructor for class org.intermine.task.CreateIndexesTask
-
- createInsertionTempTable(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Create a temporary table from pairs of insertions (eg.
- createIntergenicRegionFeatures() - Method in class org.intermine.bio.postprocess.IntergenicRegionUtil
-
Create IntergenicRegion objects
- createIntergenicRegionFeatures(Set<Location>, Map<Integer, Set<Gene>>, Integer) - Method in class org.intermine.bio.postprocess.IntergenicRegionUtil
-
Return an iterator over a Set of IntergenicRegion objects that don't
overlap the Locations in the locationSet argument.
- createIntronFeatures() - Method in class org.intermine.bio.postprocess.IntronUtil
-
Create Intron objects
- createIntronFeatures(Set<Location>, SequenceFeature, Location, Gene) - Method in class org.intermine.bio.postprocess.IntronUtil
-
Return a set of Intron objects that don't overlap the Locations
in the locationSet argument.
- createIsoformEntry(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
no:
features
gene items, just identifiers - for memory reasons
sequence, length, molecular weight, md5checksum
components - per rachel
isoforms - per mike
- createItem(GFF3Converter) - Method in class org.intermine.bio.dataconversion.GFF3SeqHandler
-
Create the sequence item from the converter.
- createItem(String) - Method in class org.intermine.dataconversion.DataConverter
-
Create item for the given class name.
- createKeyStore() - Method in class org.intermine.web.task.KeyStoreTask
-
Create and return the configured key-store.
- createList(Query) - Static method in class org.intermine.objectstore.query.ConstraintHelper
-
Converts a constraint from a query into a List of Constraint objects.
- createList(Query, FromElement) - Static method in class org.intermine.objectstore.query.ConstraintHelper
-
Return a List of Constraint objects that relate to the given FromElement.
- createList(ListService.ListCreationInfo) - Method in class org.intermine.webservice.client.services.ListService
-
Create a new list on the server by specifying its content.
- createLocatedGenesTempTable(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Create a temporary table containing the ids of the located genes.
- CreateLocationOverlapIndex - Class in org.intermine.bio.postprocess
-
Create an index on the location table to be used for range queries.
- CreateLocationOverlapIndex(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.CreateLocationOverlapIndex
-
Construct a new CreateLocationRange
- createLocations(GFF3Record) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Return true if Location objects should be made for all features (which is the default).
- createNewProfile(String, String) - Method in class org.intermine.api.profile.ProfileManager
-
Create a new profile in db with username and password given in input
- createObject(String) - Method in class org.intermine.dataloader.DirectDataLoader
-
Create a new object of the given class name and give it a unique ID.
- createObject(Class<C>) - Method in class org.intermine.dataloader.DirectDataLoader
-
Create a new object of the given class and give it a unique ID.
- createObject(Set<? extends Class<?>>) - Static method in class org.intermine.util.DynamicUtil
-
Create a DynamicBean from a Set of Class objects
- createObject(Class<C>) - Static method in class org.intermine.util.DynamicUtil
-
Create a new object given a class (not an interface).
- createObjectStoreBag() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Returns a new empty ObjectStoreBag for this ObjectStore, delegate to internal
ObjectStoreWriter.
- createObjectStoreBag() - Method in interface org.intermine.objectstore.ObjectStore
-
Returns a new empty ObjectStoreBag object that is valid for this ObjectStore.
- createObjectStoreBag() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Creates a new empty ObjectStoreBag object that is valid for this ObjectStore.
- createObjectStoreBag() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Returns a new empty ObjectStoreBag object that is valid for this ObjectStore.
- createOverlapRelations(List<String>, boolean) - Method in class org.intermine.bio.postprocess.CalculateLocations
-
Deprecated.
You should be using the create-overlap-view task instead
- createOverlaps(ObjectStore, SequenceFeature, List<?>, boolean, ObjectStoreWriter, Map<String, Integer>) - Static method in class org.intermine.bio.postprocess.OverlapUtil
-
Creates OverlapRelations for overlapping SequenceFeature objects that are located
on the given subject (generally a Chromosome).
- createPasswordChangeToken(String) - Method in class org.intermine.api.profile.ProfileManager
-
Creates a password change token assigned to the given username that will expire after a day.
- createPathConstraint(PathConstraint, String) - Method in class org.intermine.api.profile.PathQueryUpdate
-
Create a pathconstraint with the same operator and value of path contraint given in input
and with the path given in input
- createPathQuery() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
-
Returns the pathquery based on the views set in config file and the bag constraint
Executed when the user selects any item in the matches column in the enrichment widget.
- createPathQuery(String) - Method in class org.intermine.webservice.client.services.QueryService
-
Constructs a PathQuery from its XML representation.
- createPathQueryView(ObjectStore, WidgetConfig) - Method in class org.intermine.web.logic.widget.Widget
-
Create a pathquery having a view composed by all items set in the view attribute
in the config file
- createPKQueriesForClass(InterMineObject, Source, boolean, ClassDescriptor) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
-
Generates a query that searches for all objects in the database equivalent to a given
example object, considering only one of it's classes.
- createPKQueriesForClass(InterMineObject, Source, boolean, ClassDescriptor) - Method in interface org.intermine.dataloader.EquivalentObjectFetcher
-
Generates a query that searches for all objects in the database equivalent to a given
example object, considering only one of it's classes.
- createPKQueriesForClass(InterMineObject, Source, boolean, ClassDescriptor) - Method in class org.intermine.dataloader.HintingFetcher
-
Generates a query that searches for all objects in the database equivalent to a given
example object, considering only one of it's classes.
- createPKQuery(InterMineObject, Source, boolean) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
-
Generates a query that searches for all objects in the database equivalent to a given
example object according to the primary keys defined for the given source.
- createPKQuery(InterMineObject, Source, boolean) - Method in interface org.intermine.dataloader.EquivalentObjectFetcher
-
Generates a query that searches for all objects in the database equivalent to a given
example object according to the primary keys defined for the given source.
- createPKQueryForPK(InterMineObject, boolean, ClassDescriptor, PrimaryKey, Source, Set<Query>) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
-
Adds a Query to handle a primary key to a Set.
- createPKQueryForPK(InterMineObject, boolean, ClassDescriptor, PrimaryKey, Source, Set<Query>) - Method in class org.intermine.dataloader.HintingFetcher
-
Adds a Query to handle a primary key to a Set.
- createPostRequest(String, ContentType) - Method in class org.intermine.webservice.client.core.Service
-
Creates POST request.
- createProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager
-
Creates a profile in the userprofile database.
- createProfileWithoutBags(Profile) - Method in class org.intermine.api.profile.ProfileManager
-
Creates a profile in the userprofile database without adding bag.
- createQueryFieldByPath(String, Query, boolean) - Method in class org.intermine.web.logic.widget.WidgetLdr
-
Create a queryField starting from the path given in input and add the contain constraints
between all the queryclass composing the path.
- createQueryForExampleObject(Model, InterMineObject, Set<String>) - Static method in class org.intermine.objectstore.query.QueryCreator
-
Generates a query that searches for all objects in the database that have the fieldnames
set to the values in the object.
- createQueryForId(Integer, Class<? extends InterMineObject>) - Static method in class org.intermine.objectstore.query.QueryCreator
-
Create a query that will retrieve an object from the objectstore, given an ID.
- createQueryForIds(Collection<Integer>, Class<? extends InterMineObject>) - Static method in class org.intermine.objectstore.query.QueryCreator
-
Create a query that will retrieve all objects with the given IDs from the objectstore.
- createQueryForQueryNodeValues(Query, QueryNode) - Static method in class org.intermine.objectstore.query.QueryCreator
-
Create a query that will list the options for a particular
field or class in a query, given the existing constraints
For example:
Original query:
SELECT c, d
FROM Company AS c, Department AS d
WHERE c.departments CONTAINS d
AND c.name LIKE 'A%'
We want to know the possible department names are that we might
want to constrain
Returned query:
SELECT DISTINCT d.name
FROM Company AS c, Department AS d
WHERE c.departments CONTAINS d
AND c.name LIKE 'A%'
- createRAMIndex(String) - Method in class org.intermine.web.autocompletion.AutoCompleter
-
create the RAMIndex for the search engine
- CreateReferences - Class in org.intermine.bio.postprocess
-
Fill in additional references/collections in genomic model
- CreateReferences(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.CreateReferences
-
Construct with an ObjectStoreWriter, read and write from same ObjectStore
- CreateSearchIndexTask - Class in org.intermine.web.task
-
Create a the Lucene keyword search index for a mine.
- CreateSearchIndexTask() - Constructor for class org.intermine.web.task.CreateSearchIndexTask
-
- createSignature() - Method in enum org.intermine.webservice.server.JWTBuilder.Algorithm
-
- createSimpleObject(Class<C>) - Method in class org.intermine.dataloader.DirectDataLoader
-
Create a 'simple object' which doesn't inherit from InterMineObject and doesn't have an id.
- createSingletons() - Method in class org.intermine.bio.chado.config.CreateCollectionAction
-
If true, create only one object of class className with each possible fieldName;
if false, multiple objects with the same value for fieldName might be created
- createSituation - Variable in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
- createSpanningLocations(String, String, String) - Method in class org.intermine.bio.postprocess.CalculateLocations
-
Create a Location that spans the locations of some child objects.
- createSQLStatement(String, String) - Method in class org.intermine.sql.logging.DatabaseWriter
-
Creates an SQL String suitable for initialising a PreparedStatement
- createSubFeatureIdTempTable(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
-
Create a temporary table of all feature_ids for a given submission.
- createSuperUser(String, String, String) - Method in class org.intermine.api.profile.ProfileManager
-
Create a super-user with the given username, password and API-key.
- createSynonym(String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioDBConverter
-
Create a new Synonym.
- createSynonym(String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
-
Create a new Synonym.
- createSynonym(Item, String, boolean) - Method in class org.intermine.bio.dataconversion.BioFileConverter
-
Create a new Synonym.
- createSynonym(String, String, boolean) - Method in class org.intermine.bio.dataconversion.BioFileConverter
-
Create a new Synonym.
- createSynonym(FeatureData, String) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Call DataConverter.createSynonym(), store the Item then record in FeatureData that we've
created it.
- createSynonym(FeatureData, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Call DataConverter.createSynonym(), store the Item then record in FeatureData that we've
created it.
- CreateSynonymAction - Class in org.intermine.bio.chado.config
-
An action that sets a Synonym.
- CreateSynonymAction() - Constructor for class org.intermine.bio.chado.config.CreateSynonymAction
-
Make a synonym
- CreateSynonymAction(Pattern) - Constructor for class org.intermine.bio.chado.config.CreateSynonymAction
-
Make a synonym and use the type from chado ("symbol", "identifier" etc.) as the Synonym
type.
- createTempBagTable(ConstraintWithBag) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Creates a temporary bag table for the given BagConstraint.
- createTempBagTable(Connection, ConstraintWithBag, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Creates a temporary bag table for the given BagConstraint.
- createTempBagTable(Connection, QueryClassBag, boolean, String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Creates a temporary bag table for the given QueryClassBag.
- createTempBagTables(Connection, Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Create temporary tables for use with Query that use bags.
- CreateTemplateAction - Class in org.intermine.web.struts
-
Action to create a new TemplateQuery from current query.
- CreateTemplateAction() - Constructor for class org.intermine.web.struts.CreateTemplateAction
-
- createToken(Profile, int) - Method in class org.intermine.webservice.server.user.DeletionTokens
-
Create a new DeletionToken
- createTrackerTable(Connection) - Method in class org.intermine.api.tracker.AbstractTracker
-
Create the table where the tracker saves data
- createTrackerTable(Connection) - Method in interface org.intermine.api.tracker.Tracker
-
Create the table where the tracker saves data
- createTrailLabel(InterMineObject, Model) - Static method in class org.intermine.web.struts.ObjectTrailController
-
Create trail element label.
- createUtrRefs() - Method in class org.intermine.bio.postprocess.CreateReferences
-
Read the UTRs collection of MRNA then set the fivePrimeUTR and threePrimeUTR fields with the
corresponding UTRs.
- createView() - Method in class org.intermine.bio.postprocess.OverlapViewTask
-
Drop the sequencefeatureoverlappingfeatures table and replace it with a view that
uses the bioseg type to calculate the overlaps.
- createWithObjects(String, Item, String, String) - Method in class org.intermine.bio.dataconversion.GoConverter
-
Given the 'with' text from a gene_association entry parse for recognised identifier
types and create Gene or Protein items accordingly.
- CreationEvent - Class in org.intermine.api.search
-
A representation of a notification a web searchable object has been created.
- CreationEvent(WebSearchable) - Constructor for class org.intermine.api.search.CreationEvent
-
Constructor.
- CSVExportForm - Class in org.intermine.web.struts
-
A form to hold options for CSV and tab separated output.
- CSVExportForm() - Constructor for class org.intermine.web.struts.CSVExportForm
-
- CSVFormatter - Class in org.intermine.webservice.server.output
-
Formats data to comma separated data format.
- CSVFormatter() - Constructor for class org.intermine.webservice.server.output.CSVFormatter
-
Construct a CSV formatter.
- CSVHttpExporter - Class in org.intermine.web.logic.export.http
-
Exporter that exports table with results in comma separated format.
- CSVHttpExporter() - Constructor for class org.intermine.web.logic.export.http.CSVHttpExporter
-
Constructor.
- CSVRowFormatter - Class in org.intermine.web.logic.export.rowformatters
-
Row formatter formats line as comma separated strings.
- CSVRowFormatter() - Constructor for class org.intermine.web.logic.export.rowformatters.CSVRowFormatter
-
Constructor.
- currentArray - Variable in class org.intermine.webservice.server.output.JSONResultsIterator
-
- currentIterator - Variable in class org.intermine.api.results.flatouterjoins.ReallyFlatIterator
-
- currentIterator - Variable in class org.intermine.util.CombinedIterator
-
- currentMap - Variable in class org.intermine.webservice.server.output.JSONResultsIterator
-
- currentNodePath - Variable in class org.intermine.pathquery.PathQueryHandler
-
- CurrentQueryAction - Class in org.intermine.web.struts
-
Action to display the query builder (if there is a current query) or redirect to
project.sitePrefix.
- CurrentQueryAction() - Constructor for class org.intermine.web.struts.CurrentQueryAction
-
- CustomOAuthProvider - Class in org.intermine.web.struts.oauth2
-
A representation of an OAuth provider which has been configured
entirely in web-properties.
- CustomOAuthProvider(Properties, String) - Constructor for class org.intermine.web.struts.oauth2.CustomOAuthProvider
-
Construct a new provider.
- CustomPrintWriter - Class in org.intermine.web.logic.export
-
Customized PrintWriter that terminates end of the lines with defined line
separator.
- CustomPrintWriter(OutputStream, String) - Constructor for class org.intermine.web.logic.export.CustomPrintWriter
-
Constructor.
- GAFRecord - Class in org.intermine.bio.io.gaf
-
A record in a BED formatted file.
- GAFRecord(String, int, int, String, int, String) - Constructor for class org.intermine.bio.io.gaf.GAFRecord
-
Constructor
The following five attributes are normally hosted in InterMine cases.
- GAFUtil - Class in org.intermine.bio.web.export
-
Utility methods for GAF format.
- GeneInfoRecord - Class in org.intermine.bio.dataconversion
-
Data structure to hold information from one row of an NCBI Entrez gene_info file.
- GeneInfoRecord(String, String, String, String, String, String, String, String, String) - Constructor for class org.intermine.bio.dataconversion.GeneInfoRecord
-
Construct information from file for one gene.
- generate(WebserviceCodeGenInfo) - Method in interface org.intermine.api.query.codegen.WebserviceCodeGenerator
-
This method will generate web service source code from a path query or template query.
- generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
-
This method will generate web service source code in Java from a path query
or template query.
- generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebserviceJavaScriptCodeGenerator
-
This method will generate code that can be run in a browser.
- generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
-
This method will generate web service source code in Perl from a path query
or template query.
- generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
-
This method will generate code that will run using the python webservice
client library.
- generate(WebserviceCodeGenInfo) - Method in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
-
- generate(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
-
Generate the output for a ClassDescriptor.
- generate(AttributeDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
-
Generates code for a single attribute.
- generate(ReferenceDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
-
Generates code for a single reference.
- generate(CollectionDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
-
Generates code for a single collection.
- generate(Query, int, int, DatabaseSchema, Database, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Converts a Query object into an SQL String.
- generate(Query, DatabaseSchema, Database, Constraint, int, Map<Object, String>) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Converts a Query object into an SQL String.
- generate() - Method in class org.intermine.objectstore.intermine.TorqueModelOutput
-
Generate a string that contains the torque data for the given schema.
- generate(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.TorqueModelOutput
-
Generate a string that describes the given ClassDescriptor.
- generate24hrKey(Profile) - Method in class org.intermine.api.profile.ProfileManager
-
Generate a day token
- generateAddCollectionElement(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
-
Generates the addCollectionElement method.
- generateApiKey(Profile) - Method in class org.intermine.api.profile.ProfileManager
-
Generate a new API access key for this profile and return it.
- generateApiKey(String) - Method in class org.intermine.dwr.AjaxServices
-
Generate a new API key for a given user.
- generateCertificate(String, PublicKey) - Method in class org.intermine.web.security.KeySigner
-
Create a self-signed X.509 Certificate
Should be eventually replaced with X509v3CertificateBuilder.
- generateClassNames(String, Model) - Static method in class org.intermine.xml.full.ItemHelper
-
Generate a package qualified class name within the specified model from a space separated
list of namespace qualified names
- generateEquals(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
-
Generate a .equals() method for the given class.
- generateFieldDescriptors(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
-
Generate all FieldDescriptors for a class/interface
- generateGetElementType(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
-
Generates the getElementType method.
- generateGetFieldType(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
-
Generates the getFieldType method.
- generateGetFieldValue(ClassDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
-
Generates the getFieldValue method.
- generateGetObject(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
-
Generates the getoBJECT method for producing NotXml.
- generateGetSet(FieldDescriptor, boolean) - Method in class org.intermine.codegen.JavaModelOutput
-
Write code for getters and setters for given field.
- generateHashCode(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
-
Generate a .hashCode() method for the given class.
- generateIndirectionTable(CollectionDescriptor) - Method in class org.intermine.objectstore.intermine.TorqueModelOutput
-
Generate an indirection table
- generateJdbcType(String) - Static method in class org.intermine.objectstore.intermine.TorqueModelOutput
-
Convert java primitive and object names to those compatible
with torque.
- generateLink(InterMineAPI, InterMineObject) - Method in class org.intermine.api.LinkRedirectManager
-
- generateListFromQuery(PathQuery, String, String, Collection<String>, Profile) - Method in class org.intermine.webservice.server.query.QueryListAppendService
-
- generateListFromQuery(PathQuery, String, String, Collection<String>, Profile) - Method in class org.intermine.webservice.server.query.QueryToListService
-
Generate a list from a pathquery.
- generateListFromQuery(PathQuery, String, String, Collection<String>, Profile) - Method in class org.intermine.webservice.server.template.TemplateListAppendService
-
- generateNewName(Set<String>, String) - Static method in class org.intermine.api.util.NameUtil
-
Generate a new name for a list.
- generatePassword() - Static method in class org.intermine.web.task.LoadDefaultTemplatesTask
-
Generate a random 8-letter String of lower-case characters
- generatePermaLink(FastPathObject, String, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.web.logic.PortalHelper
-
Generate a perma-link to a report page for an InterMine object.
- generatePermaPath(FastPathObject, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.web.logic.PortalHelper
-
Generate a link suitable for use as an external, permanent link, in that the link should work
between rebuilds of the database.
- generatePortalLink(FastPathObject, InterMineAPI, HttpServletRequest) - Static method in class org.intermine.web.logic.PortalHelper
-
Generate a stable link to a report page for the given object, this will create a portal link
with the correct class and a value from a non-null class key field of the object.
- generatePortalPath(FastPathObject, InterMineAPI) - Static method in class org.intermine.web.logic.PortalHelper
-
Generate an external portal link (perma-link) for an InterMine object.
- generateQueryForId(Integer, Class<?>, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Generates a query to retrieve a single object from the database, by id.
- generateRandomUniqueString() - Static method in class org.intermine.api.util.TextUtil
-
- generateRandomUniqueString(int) - Static method in class org.intermine.api.util.TextUtil
-
- generateReadOnlyAccessToken(Profile, String) - Method in class org.intermine.api.profile.ProfileManager
-
Return a permanent user access token, with ReadOnly permission.
- generateReportLink(ResultElement, String) - Static method in class org.intermine.web.logic.PortalHelper
-
Generate a link to the object details page using the internal id.
- generateReportPath(ResultCell) - Static method in class org.intermine.web.logic.PortalHelper
-
Get the path fragment (starting with "/") for the report page for an object in the mine.
- generateSetFieldValue(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
-
Generates the setFieldValue method.
- generateSetObject(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
-
Generates the setoBJECT method for deserialising objects.
- generateSingleUseKey(Profile) - Method in class org.intermine.api.profile.ProfileManager
-
Generate a single use API key and store it in memory, before returning it.
- generateSql(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Generate sql from a Query
- generateSql(Connection, Query, int, int) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Create temporary tables for the bag in the BagConstraints of the given Query, then call
SqlGenerator.generate().
- generateSql(Connection, Query, int, int) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Create temporary tables for the bag in the BagConstraints of the given Query, then call
SqlGenerator.generate().
- generateSqlCompatibleName(String) - Static method in class org.intermine.sql.DatabaseUtil
-
Convert any sql keywords to valid names for tables/columns.
- generateToString(ClassDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
-
Generate a .toString() method for the given class .
- generationSqlString - Variable in class org.intermine.sql.precompute.PrecomputedTable
-
- geneType - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
-
- GenomeDBConverter - Class in org.intermine.bio.dataconversion
-
A ChadoDBConverter that sets the dataset and datasource for genome databases (eg.
- GenomeDBConverter(Database, Model, ItemWriter) - Constructor for class org.intermine.bio.dataconversion.GenomeDBConverter
-
Create a new ChadoDBConverter object.
- get(int) - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
- get(int) - Method in class org.intermine.api.results.WebResults
- get(int) - Method in class org.intermine.objectstore.query.Results
- get(Object) - Method in class org.intermine.util.AlwaysMap
- get(Object) - Method in class org.intermine.util.IdentityMap
- get(int) - Method in class org.intermine.util.IntToIntMap
-
Retrieves a mapping from the object
- get(Integer) - Method in class org.intermine.util.IntToIntMap
-
Retrieves a mapping from the object.
- get(Object) - Method in class org.intermine.util.ReferenceMap
- get(Path, Profile, PathQuery) - Method in class org.intermine.web.logic.query.DisplayConstraintFactory
-
Get a display constraint.
- get(PathConstraint, Profile, PathQuery) - Method in class org.intermine.web.logic.query.DisplayConstraintFactory
-
Get a display constraint.
- get(Object) - Method in class org.intermine.web.logic.results.ReportObjectFactory
-
Get a ReportObject for the given InterMineObject.
- get(String) - Method in class org.intermine.web.security.KeyStorePublicKeySource
-
- get(String) - Method in interface org.intermine.web.security.PublicKeySource
-
Get a specific key by name.
- get(int) - Method in class org.intermine.webservice.client.lists.ItemList
-
Get an item by its index.
- get(int) - Method in class org.intermine.webservice.client.results.JsonRow
-
- get(Object) - Method in class org.intermine.webservice.client.results.JsonRowMap
-
- get(int) - Method in class org.intermine.webservice.client.results.ResultRowList
-
- get(Object) - Method in class org.intermine.webservice.client.results.ResultRowMap
-
- getAbbreviation() - Method in class org.intermine.bio.util.OrganismData
-
Get the abbreviation of this organism.
- getAbbreviation(String) - Static method in class org.intermine.webservice.server.CodeTranslator
-
Returns corresponding abbreviation of translated operation.
- getAcceptableFormats(HttpServletRequest) - Static method in class org.intermine.webservice.server.WebServiceRequestParser
-
Get the list of formats that this request finds acceptable.
- getAccepted() - Method in class org.intermine.api.bag.SharingInvite
-
- getAccepted() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
-
- getAcceptedAt() - Method in class org.intermine.api.bag.SharingInvite
-
- getAcceptedAt() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
-
- getAccessCounter(Connection) - Method in class org.intermine.api.tracker.TemplateTracker
-
Return the number of executions for each public template
- getAccessCounter() - Method in class org.intermine.api.tracker.TrackerDelegate
-
Return the rank associated to the templates
- getAccessibleLists() - Method in class org.intermine.webservice.client.services.ListService
-
Returns all the lists that this service has access to.
- getAccessions() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getAction() - Method in class org.intermine.api.search.TaggingEvent
-
- getAction() - Method in class org.intermine.web.struts.WidgetForm
-
- getActionMessage(String, int, String, String) - Method in class org.intermine.web.logic.bag.BagConverter
-
Get the ActionMessage to display in the webapp
- getActionMessage() - Method in exception org.intermine.web.struts.oauth2.ForseenProblem
-
Get a struts action message, rather than a simple string message.
- getActionType() - Method in class org.intermine.web.struts.TemplateSettingsForm
-
- getAddIssues() - Method in class org.intermine.webservice.server.lists.ListCreationInput
-
- getAdditionalBeanInfo() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
-
- getAdditionalBeanInfo() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
-
- getAdditionalConverters(String) - Method in class org.intermine.api.bag.BagQueryConfig
-
Return a Map from a converter Class name (such as
org.intermine.bio.web.logic.OrthologueConverter) to set of additional converters.
- getAdditionalFields() - Method in class org.intermine.web.search.KeywordSearchResult
-
additional display field expressions
- getAdditionalParameter(HttpServletRequest, String) - Static method in class org.intermine.web.logic.PortalHelper
-
Searches a request for additional parameters that might match an additional converter.
- getAlgorithm() - Method in enum org.intermine.web.logic.widget.ErrorCorrection.Strategy
-
- getAlias() - Method in class org.intermine.sql.query.AbstractTable
-
Returns the alias for this AbstractTable object.
- getAlias() - Method in class org.intermine.sql.query.SelectValue
-
Gets the alias from this object.
- getAliasedColumnHeaders(PathQuery, WebConfig) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
-
Get the view for a path query reformatted to obey the labels given in webconfig.
- getAliases() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return all values of the Alias field from the attributes of this record.
- getAliases() - Method in class org.intermine.objectstore.query.Query
-
Returns the map of QuerySelectables and FromElements to String aliases
- getAll() - Method in class org.intermine.web.security.KeyStorePublicKeySource
-
- getAll() - Method in interface org.intermine.web.security.PublicKeySource
-
- getAllBags() - Method in class org.intermine.api.profile.Profile
-
Get all bags associated with this profile, both valid and invalid.
- getAllChildren() - Method in class org.intermine.bio.chado.ChadoCVTerm
-
Return a Set of all the child ChadoCVTerms of this term.
- getAllClassDescriptors() - Method in class org.intermine.xml.full.Item
-
Return the ClassDescriptors of the class of this Item (as given by className) and all the
implementations.
- getAllCVTerms() - Method in class org.intermine.bio.chado.ChadoCV
-
Return a Set of all the CVTerms in this CV.
- getAlleleCVTermsResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Get result set of feature_id, cvterm_id pairs for the alleles in flybase chado.
- getAllelePropPubResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Return a result set containing the featureprop_id and the publication identifier of the
featureprops for al alleles.
- getAllelePropResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Return a result set containing the alleles and their featureprops.
- getAllJSONResults(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Returns all the results for the given template template,
as JSON objects (see @link {http://www.intermine.org/wiki/JSONObjectFormat}).
- getAllJSONResults(String) - Method in class org.intermine.webservice.client.services.QueryService
-
Fetch all the results as a list of JSON Objects
- getAllJSONResults(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
-
Returns all the results for the given template template with the given parameters,
as JSON objects (see @link {http://www.intermine.org/wiki/JSONObjectFormat}).
- getAllNullAttributes() - Method in class org.intermine.objectstore.ObjectStoreSummary
-
Get a list of the attributes that are always null or empty.
- getAllNullReferencesAndCollections() - Method in class org.intermine.objectstore.ObjectStoreSummary
-
Get a list of reference and collection names that are always null or empty.
- getAllParents() - Method in class org.intermine.bio.chado.ChadoCVTerm
-
Return a Set of all the parent ChadoCVTerms of this term.
- getAllParents() - Method in class org.intermine.bio.postprocess.PopulateChildFeatures
-
- getAllPartOfs(String) - Method in class org.intermine.bio.ontology.SequenceOntology
-
- getAllReportDisplayersForType(String) - Method in class org.intermine.web.displayer.DisplayerManager
-
Get all displayers for the given type regardless of placement.
- getAllResults(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Returns all the results for the given template template.
- getAllResults(String) - Method in class org.intermine.webservice.client.services.QueryService
-
Returns all of the results of the specified PathQuery.
- getAllResults(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
-
Returns all the results for the given template template with the given parameters.
- getAllRowIterator(String) - Method in class org.intermine.webservice.client.services.QueryService
-
Returns all the results of a specified PathQuery as an iterator.
- getAllRows() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Return all the resultElementRows of the table as a List of Lists.
- getAllRowsIterator(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Returns an iterator over all the rows for the template.
- getAllRowsIterator(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
-
Returns all the rows for the template when run with the given parameters.
- getAllSelected() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
- getAllSelectedColumn() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
If a whole column is selected, return its index, otherwise return -1.
- getAllSuperUsers() - Method in class org.intermine.api.profile.ProfileManager
-
- getAlteredViews(PathQuery) - Static method in class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj
-
Get the views for the transformed query.
- getAnalysedTotal() - Method in class org.intermine.web.logic.widget.EnrichmentResults
-
Get the number of items in the sample that had an attribute value.
- getAnnotatedCountsInPopulation() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
-
For each attribute give a count of items in the whole population that have that attribute
assigned to them, M.
- getAnnotatedCountsInPopulation() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
-
- getAnnotatedCountsInSample() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
-
For each attribute give a count of items in the sample that have that attribute assigned to
them, k.
- getAnnotatedCountsInSample() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
-
- getApiKey() - Method in class org.intermine.api.profile.Profile
-
- getAPIVersion() - Method in class org.intermine.webservice.client.core.Service
-
- getAppendConfig() - Method in class org.intermine.web.logic.config.HeaderConfigTitle
-
- getApplicationName() - Method in class org.intermine.webservice.client.core.Service
-
- getAppliedData(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the rows needed for data from the applied_protocol_data table.
- getAppliedDataAll(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the rows needed for data from the applied_protocol_data table.
- getAppliedDataAttributes(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Query to get data attributes.
- getAppliedDataCharacteristics(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the rows needed for data from the applied_protocol_data table.
- getAppliedProtocols(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the rows needed from the appliedProtocol table.
- getApproximateType() - Method in class org.intermine.objectstore.query.QueryCast
-
Returns an integer representing the approximate type of this QueryEvaluable, in the case
where an accurate type cannot be ascertained.
- getApproximateType() - Method in interface org.intermine.objectstore.query.QueryEvaluable
-
Returns an integer representing the approximate type of this QueryEvaluable, in the case
where an accurate type cannot be ascertained.
- getApproximateType() - Method in class org.intermine.objectstore.query.QueryExpression
-
Returns an integer representing the approximate type of this QueryEvaluable, in the case
where an accurate type cannot be ascertained.
- getApproximateType() - Method in class org.intermine.objectstore.query.QueryField
-
Returns an integer representing the approximate type of this QueryEvaluable, in the case
where an accurate type cannot be ascertained.
- getApproximateType() - Method in class org.intermine.objectstore.query.QueryForeignKey
-
Returns an integer representing the approximate type of this QueryEvaluable, in the case
where an accurate type cannot be ascertained.
- getApproximateType() - Method in class org.intermine.objectstore.query.QueryFunction
-
Returns an integer representing the approximate type of this QueryEvaluable, in the case
where an accurate type cannot be ascertained.
- getApproximateType() - Method in class org.intermine.objectstore.query.QueryValue
-
Returns an integer representing the approximate type of this QueryEvaluable, in the case
where an accurate type cannot be ascertained.
- getApproximateType() - Method in class org.intermine.objectstore.query.UnknownTypeValue
-
Returns the approximate type of the argument.
- getArg1() - Method in class org.intermine.objectstore.query.ClassConstraint
-
Returns the QueryClass argument 1
- getArg1() - Method in class org.intermine.objectstore.query.QueryExpression
-
Returns the left argument of the expression.
- getArg1() - Method in class org.intermine.objectstore.query.SimpleConstraint
-
Returns the left argument of the constraint.
- getArg2() - Method in class org.intermine.objectstore.query.QueryExpression
-
Returns the right argument, or the position argument of the substring.
- getArg2() - Method in class org.intermine.objectstore.query.SimpleConstraint
-
Returns the right argument of the constraint.
- getArg2Object() - Method in class org.intermine.objectstore.query.ClassConstraint
-
Returns the Object argument 2
- getArg2QueryClass() - Method in class org.intermine.objectstore.query.ClassConstraint
-
Returns the QueryClass argument 2
- getArg3() - Method in class org.intermine.objectstore.query.QueryExpression
-
Returns the length argument of a substring expression.
- getAspect(String) - Static method in class org.intermine.api.tag.AspectTagUtil
-
Extracts aspect from tag name.
- getAspectDisplayers() - Method in class org.intermine.web.logic.config.Type
-
- getAspects() - Method in class org.intermine.web.logic.config.Displayer
-
Get the aspects of this displayer
- getAspects(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Returns the Map of aspects.
- getAspectSources() - Method in class org.intermine.web.logic.aspects.Aspect
-
Get the AspectSources.
- getAspectTemplates(String) - Method in class org.intermine.api.template.TemplateManager
-
Get public templates for a particular aspect.
- getAspectTemplates(String, Integer) - Method in class org.intermine.api.template.TemplateManager
-
Get public templates for a particular aspect.
- getAttribute() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
the identifier is only held until the next line of the XML is processed, at which
point the item is stored
- getAttribute(String) - Static method in class org.intermine.web.context.InterMineContext
-
Get the value of a stored attribute.
- getAttribute(String) - Method in class org.intermine.xml.full.Item
-
Get a named attribute.
- GetAttributeAsFileAction - Class in org.intermine.web.struts
-
Provide an attribute value as a file
- GetAttributeAsFileAction() - Constructor for class org.intermine.web.struts.GetAttributeAsFileAction
-
- getAttributeDescriptors() - Method in class org.intermine.web.logic.results.ReportObject
-
Get attribute descriptors.
- getAttributeIndexStatements(ClassDescriptor, Map<String, IndexStatement>) - Method in class org.intermine.task.CreateIndexesTask
-
Add indexes for all fields to the relevant tables for a given ClassDescriptor.
- getAttributeOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Gets the value of attributeOp
- getAttributeOps() - Method in class org.intermine.web.struts.TemplateForm
-
Get the attribute ops
- getAttributeOps(String) - Method in class org.intermine.web.struts.TemplateForm
-
Get an attribute op
- getAttributeOptions() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Gets the value of attributeValue
- getAttributes() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the attributes of this record as a Map from attribute key to Lists of attribute
values.
- getAttributes() - Method in class org.intermine.objectstore.intermine.DatabaseSchema.Fields
-
Returns the Set of attributes
- getAttributes() - Method in class org.intermine.web.logic.results.ReportObject
-
Get the attribute fields and values for this object
- getAttributes() - Method in class org.intermine.xml.full.Item
-
Get all the attributes.
- getAttributesFromBag(InterMineBag, ObjectStore, String, String, String) - Static method in class org.intermine.web.logic.bag.BagHelper
-
- getAttributesFromBag(InterMineBag, ObjectStore, String, String) - Static method in class org.intermine.web.logic.bag.BagHelper
-
Used by esyn tool
- getAttributeValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Gets the value of attributeValue
- getAttributeValues() - Method in class org.intermine.web.struts.TemplateForm
-
Get the attribute values
- getAttributeValues(String) - Method in class org.intermine.web.struts.TemplateForm
-
Get an attribute value
- getAuthenticatedUser() - Method in class org.intermine.webservice.server.WebService
-
Get a profile that is a true authenticated user that exists in the
database.
- getAutoCompleter() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Return the autocompleter for this path if one is available.
- getAutoCompleter(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Get the AutoCompleter stored on the ServletContext.
- getAverage() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary
-
- getBag(Profile, String) - Method in class org.intermine.api.bag.BagManager
-
Fetch a global or user or shared bag by name.
- getBag() - Method in class org.intermine.api.bag.SharingInvite
-
- getBag() - Method in class org.intermine.objectstore.query.BagConstraint
-
Get the bag Collection.
- getBag() - Method in interface org.intermine.objectstore.query.ConstraintWithBag
-
Returns the bag that the constraint is using.
- getBag() - Method in class org.intermine.objectstore.query.MultipleInBagConstraint
-
Returns the bag that this object was constructed with.
- getBag() - Method in class org.intermine.objectstore.query.QueryClassBag
-
Returns the bag of objects.
- getBag() - Method in class org.intermine.pathquery.PathConstraintBag
-
Returns the bag name that the constraint is constraining to.
- getBag() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
the bag that this widget is using
- getBag(String) - Method in class org.intermine.web.struts.TemplateForm
-
Get the bag name selected.
- getBagConverter(InterMineAPI, WebConfig, String) - Static method in class org.intermine.web.logic.PortalHelper
-
Returns a BagConverter for the given parameters.
- getBagCreationQuery() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Return a Query that produces a Results object of the selected objects.
- getBagDisplayers() - Method in class org.intermine.web.logic.config.Type
-
Get the List of bag Displayers
- getBagId() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
-
- getBagId() - Method in class org.intermine.objectstore.query.ObjectStoreBag
-
Returns the identifier of the bag.
- getBagManager() - Method in interface org.intermine.api.API
-
- getBagManager() - Method in class org.intermine.api.InterMineAPI
-
- getBagManager() - Static method in class org.intermine.api.query.PathQueryAPI
-
Returns a BagManager.
- getBagName() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- getBagName() - Method in class org.intermine.web.struts.FindInListForm
-
- getBagName() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
-
Get the value of bagName
- getBagName() - Method in class org.intermine.web.struts.WidgetForm
-
- getBagName() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
-
Get the type of the bag
- getBagNames() - Method in class org.intermine.pathquery.PathQuery
-
Returns all bag names used in constraints on this query.
- getBagOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Gets the value of bagOp
- getBagOp(String) - Method in class org.intermine.web.struts.TemplateForm
-
Get the bag operation selected.
- getBagOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Return the valid constraint ops when constraining on a bag.
- getBagQueries(String) - Method in class org.intermine.api.bag.BagQueryConfig
-
Return a list of BagQuerys to run for a given type
- getBagQueries() - Method in class org.intermine.api.bag.BagQueryHandler
-
Return the bag queries from the XML file.
- getBagQueryConfig() - Method in interface org.intermine.api.API
-
- getBagQueryConfig() - Method in class org.intermine.api.bag.BagQueryHandler
-
Return the BagQueryConfig created from the XML.
- getBagQueryConfig() - Method in class org.intermine.api.InterMineAPI
-
- getBagQueryConfig() - Static method in class org.intermine.api.query.PathQueryAPI
-
Returns a BagQueryConfig configured in WEB-INF/bag-queries.xml.
- getBagQueryResult() - Method in class org.intermine.api.bag.BagQueryUpgrade
-
- getBagQueryRunner() - Method in interface org.intermine.api.API
-
- getBagQueryRunner() - Method in class org.intermine.api.InterMineAPI
-
The bag-query runner is the object that performs look-up queries used when
constructing bags from lists of identifiers, and in path-queries when
LOOKUP constraints are used.
- getBags(Profile) - Method in class org.intermine.api.bag.BagManager
-
Fetch all global bags, user bags and shared bags combined in the same map.
- getBags() - Method in class org.intermine.api.bag.operations.BagOperation
-
- getBags() - Method in class org.intermine.api.profile.BagSet
-
- getBags() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
-
Returns the List of bags.
- getBags() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
-
Returns the Collection of bags.
- getBags() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Get a list of public and user bag names available and currentfor this path.
- getBagsAndClasses(Set<ClassDescriptor>, Set<InterMineBag>, Profile, BagManager, Model, String[]) - Static method in class org.intermine.webservice.server.lists.ListServiceUtils
-
Given an array of bag names, populate both a set of bags, and a set of class-descriptors
with the objects these names refer to.
- getBagsOfType(Profile, String) - Method in class org.intermine.api.bag.BagManager
-
Fetch global and user bags of the specified type or a subclass of the specified type.
- getBagsOfType(Profile, String, boolean) - Method in class org.intermine.api.bag.BagManager
-
Fetch global and user bags of the specified type or a subclass of the specified type.
- getBagTableNames() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- getBagType() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Returns the bag type that the constraint can be constrained to.
- getBagType() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- getBagType() - Method in class org.intermine.web.struts.BagUploadConfirmForm
-
Get the bag type - hidden form value.
- getBagType() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- getBagType() - Method in class org.intermine.web.struts.WidgetForm
-
- getBagValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Gets the value of bagValue
- getBaseEof() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Returns the base equivalent object fetcher.
- getBaseLink() - Method in class org.intermine.web.tags.table.NavigationBarTag
-
- getBaseUrl() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
-
- getBaseUrl(HttpServletRequest) - Static method in class org.intermine.web.logic.PortalHelper
-
Get the base url for this web-app.
- getBaseURL() - Method in class org.intermine.web.util.AttributeLinkURL
-
- getBaseURL() - Method in class org.intermine.web.util.URLGenerator
-
- getBatch(int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
-
Gets a batch by whatever means - maybe batches, maybe the ObjectStore.
- getBatchFromCache(int) - Method in class org.intermine.objectstore.query.ResultsBatches
-
Returns the given batch, if it is already in the batch cache.
- getBatchNoForRow(int) - Method in class org.intermine.objectstore.query.Results
-
Gets the batch for a particular row
- getBatchNoForRow(int) - Method in class org.intermine.objectstore.query.ResultsBatches
-
Gets the batch for a particular row
- getBatchSize() - Method in class org.intermine.objectstore.query.Results
-
Gets the batch size being used.
- getBatchSize() - Method in class org.intermine.objectstore.query.ResultsBatches
-
Gets the batch size being used.
- getBeanDescriptor() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
-
- getBeanDescriptor() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
-
- getBest() - Method in class org.intermine.sql.precompute.BestQueryExplainer
-
Gets the best Candidate found so far.
- getBestExplainResult() - Method in class org.intermine.sql.precompute.BestQueryExplainer
-
Gets the ExpainResult for the best Query found so far.
- getBestExplainResult() - Method in class org.intermine.sql.precompute.BestQueryFallback
-
Gets the ExpainResult for the best Query found so far
- getBestQuery() - Method in class org.intermine.sql.precompute.BestQuery
-
Gets the best Query found so far
- getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryExplainer
-
Gets the best Query found so far
- getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryFallback
-
Gets the best Query found so far
- getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryLogger
-
Gets the best Query found so far
- getBestQuery() - Method in class org.intermine.sql.precompute.BestQueryStorer
-
Gets the best Query found so far
- getBestQuery() - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery
-
Gets the best Query found so far
- getBestQueryString() - Method in class org.intermine.sql.precompute.BestQuery
-
Gets the best query String found so far
- getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryExplainer
-
Gets the best query String found so far.
- getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryFallback
-
Gets the best query String found so far
- getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryLogger
-
Gets the best query String found so far
- getBestQueryString() - Method in class org.intermine.sql.precompute.BestQueryStorer
-
Gets the best query String found so far
- getBestQueryString() - Method in class org.intermine.sql.precompute.EncloseSubqueryBestQuery
-
Gets the best query String found so far
- getBgcolor() - Method in class org.intermine.api.mines.LocalMine
-
- getBgcolor() - Method in interface org.intermine.api.mines.Mine
-
- getBgcolor() - Method in class org.intermine.api.mines.RemoteMine
-
- getBinaryIndexMap() - Method in class org.intermine.web.autocompletion.AutoCompleter
-
Returns byte array of the RAMIndexMap
- getBinsParam() - Method in class org.intermine.objectstore.query.WidthBucketFunction
-
- getBlockCount() - Method in class org.intermine.bio.io.bed.BEDRecord
-
- getBlockCount() - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- getBlockSizes() - Method in class org.intermine.bio.io.bed.BEDRecord
-
- getBlockSizes() - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- getBlockStarts() - Method in class org.intermine.bio.io.bed.BEDRecord
-
- getBlockStarts() - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- getBoolean(String) - Method in class org.intermine.webservice.client.results.Item
-
Get a property known to be an boolean.
- getBuffer() - Method in class org.intermine.sql.writebatch.PostgresByteArrayOutputStream
-
Returns the byte buffer without copying it.
- getBuildMode() - Method in class org.intermine.api.tracker.track.ListTrack
-
Return the way the list is built
- getButton() - Method in class org.intermine.web.logic.query.MetadataNode
-
Gets the value of button
- getByChadoId(Integer) - Method in class org.intermine.bio.chado.ChadoCV
-
Return the ChadoCVTerm object for a given cvterm_id.
- getByToken(InterMineAPI, String) - Static method in class org.intermine.api.bag.SharingInvite
-
- getCallback() - Method in class org.intermine.webservice.server.WebService
-
Get the value of the callback parameter.
- getCanCreateConstraint() - Method in class org.intermine.web.logic.query.MetadataNode
-
Returns true if there is any possibility of creating a constraint on this path.
- getCandidateLoops(String) - Method in class org.intermine.pathquery.PathQuery
-
Returns the set of paths that could feasibly be loop constrained onto the given path, given
the current outer join situation.
- getCandidateLoops() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Returns the set of paths that could feasibly be loop constrained onto the constraint's path,
given the query's outer join situation.
- getCaseSensitive() - Method in interface org.intermine.api.idresolution.JobInput
-
- getCaseSensitive() - Method in class org.intermine.web.logic.bag.WebJobInput
-
- getCaseSensitive() - Method in class org.intermine.web.struts.BuildBagForm
-
- getCategories(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Gets the aspect categories from the servlet context.
- getCategory() - Method in class org.intermine.sql.precompute.PrecomputedTable
-
Returns the category of this PrecomputedTable
- getCategoryPath() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- getCauseElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
-
- getCauseElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
-
- getCDNALengthResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Return a result set containing the feature_id and its seqlen
The method is protected so that is can be overridden for
testing.
- getChadoCV(String) - Method in class org.intermine.bio.chado.ChadoCVFactory
-
Get a new ChadoCV containing only cv terms from the cv with the given name.
- getChadoDBConverter() - Method in class org.intermine.bio.dataconversion.ChadoProcessor
-
Return the ChadoDBConverter that was passed to the constructor.
- getChadoIdToOrgDataMap() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
-
Return a map from chado organism_id to OrganismData object for all the organisms that we
are processing
- getChadoOrganismIds(Connection) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
-
Return a map from chado organism id to OrganismData for the organisms in the organism table
in chado.
- getCharSet() - Method in class org.intermine.webservice.client.core.ContentType
-
- getChartType() - Method in class org.intermine.webservice.client.widget.Widget
-
- getChartWidgets() - Method in class org.intermine.webservice.client.services.WidgetService
-
- getChildId() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
-
Get childId value
- getChildren() - Method in class org.intermine.pathquery.LogicExpression.Operator
-
Get an unmodifiable copy of the node's children.
- getChildren(ClassDescriptor) - Static method in class org.intermine.web.struts.InitialiserPlugin
-
Get the names of the type of this ClassDescriptor and all its descendants
- getChildren(ClassDescriptor, Set<String>) - Static method in class org.intermine.web.struts.InitialiserPlugin
-
Add the names of the descendents of a ClassDescriptor to a Set
- getChildTermId() - Method in class org.intermine.bio.ontology.OboRelation
-
- getChrom() - Method in class org.intermine.bio.io.bed.BEDRecord
-
- getChrom() - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- getChromEnd() - Method in class org.intermine.bio.io.bed.BEDRecord
-
- getChromEnd() - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- getChromosome(String, int) - Method in class org.intermine.bio.dataconversion.BioDBConverter
-
Make a Chromosome Item, then store and return it.
- getChromosome(String, Organism) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
-
Return a Chromosome object for the given item.
- getChromosomeFeatureMap(Integer) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Fetch the populated map of chromosome-like features.
- getChromosomeFeatureTypes() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Get a list of the chado/so types of the Chromosome-like objects we wish to load.
- getChromosomeStructureVariationResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Return the results of running a query for the chromosome_structure_variation feature types.
- getChromStart() - Method in class org.intermine.bio.io.bed.BEDRecord
-
- getChromStart() - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- getClassConfig() - Method in class org.intermine.web.logic.config.FieldConfig
-
- getClassCount(String) - Method in class org.intermine.objectstore.ObjectStoreSummary
-
Get the number of instances of a particular class in the ObjectStore.
- getClassDescriptor() - Method in class org.intermine.web.logic.results.ReportObject
-
Get the class descriptor for this object
- getClassDescriptorByName(String) - Method in class org.intermine.xml.full.Item
-
Throw a RuntimeException if any of the named class isn't in the Model set by setModel().
- getClassDescriptors() - Method in class org.intermine.api.profile.InterMineBag
-
Return the class descriptors for the type of this bag.
- getClasses() - Method in class org.intermine.api.bag.operations.BagOperation
-
- getClassesForBags(Collection<InterMineBag>) - Method in class org.intermine.webservice.server.lists.AbstractListService
-
Get the classes represented by a collection of bags.
- getClassFieldConfigs(WebConfig, ClassDescriptor) - Static method in class org.intermine.web.logic.config.FieldConfigHelper
-
Find the FieldConfig objects for the the given ClassDescriptor (or generate them).
- getClassFieldConfigs(ClassDescriptor) - Method in class org.intermine.web.logic.results.InlineResultsTable
-
Find the FieldConfig objects for the the given ClassDescriptor.
- getClassIndex(List<Class<?>>, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper
-
- getClassIndexes(List<Class<?>>, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper
-
- getClassKeys() - Method in interface org.intermine.api.API
-
- getClassKeys() - Method in class org.intermine.api.bag.operations.BagOperation
-
- getClassKeys() - Method in class org.intermine.api.InterMineAPI
-
The class keys are the list of fields used to identify objects in the data
base, so for Employee it would include "name", and for Gene it would include
"symbol".
- getClassKeys() - Static method in class org.intermine.api.query.PathQueryAPI
-
Returns classkeys configured in class_keys.properties.
- getClassKeys() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
Get the classKeys
- getClassName() - Method in class org.intermine.api.bag.AdditionalConverter
-
- getClassName() - Method in class org.intermine.bio.chado.config.CreateCollectionAction
-
Return the className that was passed to the constructor.
- getClassName() - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
Return the class name set with setClassName().
- getClassName() - Method in class org.intermine.web.autocompletion.LuceneObjectClass
-
getClassName
- getClassName() - Method in class org.intermine.web.logic.config.TableExportConfig
-
Get the class name of the exporter eg. org.intermine.bio.web.export.SequenceHttpExporter
- getClassName() - Method in class org.intermine.web.logic.config.Type
-
Get the class name
- getClassName() - Method in class org.intermine.web.logic.results.InlineResultsTableRow
-
- getClassName() - Method in class org.intermine.web.logic.results.InlineTableResultElement
-
- getClassName() - Method in class org.intermine.web.struts.QueryClassSelectForm
-
Get the class name
- getClassName() - Method in class org.intermine.xml.full.Item
-
Get the class name of this item.
- getClassName(Object, Model) - Static method in class org.intermine.xml.XmlHelper
-
Get the class name if object represents a material class in model.
- getClassNames() - Method in class org.intermine.bio.dataconversion.IdResolver
-
Return a set of class names the reslover holds
- getClassNames(ObjectStore, String) - Static method in class org.intermine.objectstore.querygen.QueryGenUtil
-
Given a String, perform a one of a set of expansions and return a Set of unqualified class
names.
- getClazz() - Method in class org.intermine.objectstore.querygen.QueryGenUtil.QueryAndClass
-
Returns the class.
- getClientId() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
-
- getClientId() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
-
- getClientId() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
-
- getClientSecret() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
-
- getClientSecret() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
-
- getClientSecret() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
-
- getClob() - Method in class org.intermine.objectstore.query.ClobAccess
-
Return the Clob that this object is accessing.
- getClob() - Method in class org.intermine.objectstore.query.PendingClob
-
Return the Clob that this object is accessing.
- getClobId() - Method in class org.intermine.objectstore.query.Clob
-
Returns the identifier of the Clob.
- getCode() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
If editing an existing constraint get the code for this constraint in the query, return null
if creating a new constraint.
- getCode() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
-
Get the code associated with this constraint in the query.
- getCode() - Method in class org.intermine.web.logic.template.ConstraintInput
-
- getCode() - Method in class org.intermine.webservice.client.template.TemplateParameter
-
- getCode(String) - Static method in class org.intermine.webservice.server.CodeTranslator
-
Returns corresponding code of translated operation.
- getCode() - Method in class org.intermine.webservice.server.output.Output
-
Gets the error code
- getCollection() - Method in class org.intermine.web.logic.results.DisplayCollection
-
- getCollection() - Method in class org.intermine.web.logic.results.ReportInList
-
- getCollection(String) - Method in class org.intermine.webservice.client.results.Item
-
Get a set of items representing the elements in a collection field on an item.
- getCollection(String) - Method in class org.intermine.xml.full.Item
-
Get a named collection.
- getCollections() - Method in class org.intermine.web.logic.results.ReportObject
-
Get the collection fields and values for this object
- getCollections() - Method in class org.intermine.xml.full.Item
-
Get all the collections.
- getColNames() - Method in class org.intermine.sql.writebatch.TableBatch
-
Returns the column names.
- getColumn() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary
-
- getColumnAliases(Query) - Static method in class org.intermine.objectstore.query.QueryHelper
-
Returns a list of aliases, where each alias corresponds to each element of the SELECT list
of the Query object.
- getColumnClasses(PagedTable) - Static method in class org.intermine.web.logic.export.ExportHelper
-
- getColumnFieldClasses() - Method in class org.intermine.task.DelimitedFileConfiguration
-
Return a List of Class objects corresponding to the fields returned by
getColumnFieldDescriptors().
- getColumnFieldDescriptors() - Method in class org.intermine.task.DelimitedFileConfiguration
-
Return a List of the configured AttributeDescriptors.
- getColumnHeaders() - Method in class org.intermine.pathquery.PathQuery
-
Returns the paths descriptions for the view.
- getColumnHeaderStyle() - Method in class org.intermine.webservice.server.WebService
-
Get an enum which represents the column header style (path, friendly, or
none)
- getColumnId() - Method in class org.intermine.api.results.Column
-
- getColumnIdentifier() - Method in class org.intermine.api.results.Column
-
Used in the view to match this element
- getColumnName(FieldDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
-
Creates a column name for a field descriptor
- getColumnNames() - Method in class org.intermine.api.results.WebResults
-
Return the names of the columns of the results.
- getColumnNames() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Return the column names
- getColumnNames() - Method in class org.intermine.web.tags.table.TableTag
-
- getColumnPaths(PagedTable) - Static method in class org.intermine.web.logic.export.ExportHelper
-
Return a List containing the Path objects from the Columns of this PagedTable.
- getColumns() - Method in class org.intermine.api.results.ExportResultsIterator
-
Allows test to access column info.
- getColumns() - Method in class org.intermine.api.results.WebResults
-
Returns the columns for these results.
- getColumns() - Method in interface org.intermine.api.results.WebTable
-
Returns the Column objects for this table.
- getColumns() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Get the list of column configurations
- getColumns() - Method in class org.intermine.web.logic.widget.TableWidget
-
Get the columns
- getColumns() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
-
Get the columnNames
- getColumns() - Method in class org.intermine.webservice.server.core.SubTable
-
- getColumnsPath() - Method in class org.intermine.api.results.WebResults
-
- getColumnsPath() - Method in interface org.intermine.api.results.WebTable
-
- getColumnsSize() - Method in class org.intermine.web.logic.results.InlineResultsTable
-
- getColumnSummary(String, String) - Static method in class org.intermine.dwr.AjaxServices
-
Get the summary for the given column
- getColumnTitle() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
- getColumnTypes(Query) - Static method in class org.intermine.objectstore.query.QueryHelper
-
Returns a list of Class objects, where each object corresponds to the type of each element
of the SELECT list of the Query object.
- getColumnTypeString(Class<?>) - Method in class org.intermine.sql.Database
-
Return the SQL type used to store objects of the given Class.
- getComment() - Method in class org.intermine.template.TemplateQuery
-
Get the private comment for this template.
- getComment() - Method in class org.intermine.web.struts.TemplateSettingsForm
-
Return the comment
- getCommentEvidence() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getComments() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getCommentType() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getCommonFeaturesMap() - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
-
Get a map of features that are expected to be common between submissions.
- getCommonJsonConstraintPrefix(String, PathConstraint) - Method in class org.intermine.pathquery.PathQuery
-
Get the JSON prefix common to all constraints.
- getCommonJsonConstraintPrefix(String, PathConstraint) - Method in class org.intermine.template.TemplateQuery
-
- getCompatibleCurrentBags(Profile, String) - Method in class org.intermine.api.bag.BagManager
-
Fetch global and user bags current of the specified type or a subclass
or any superclass of the specified type.
- getComplete() - Method in class org.intermine.objectstore.query.ResultsInfo
-
Returns the estimated amount of time taken to produce the entire set of results.
- getComplete() - Method in class org.intermine.sql.query.ExplainResult
-
Returns the number of page requests before the query is completed, estimated by the
database for this query.
- getCompletedProcessors() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
-
- getComponents() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getComponentsForQuery(Query) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Returns a Set of independent components that affect the results of the given Query.
- getComponentsForQuery(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Returns a Set of independent components that affect the results of the given Query.
- getComponentsForQuery(Query) - Method in interface org.intermine.objectstore.ObjectStore
-
Returns a Set of independent components that affect the results of the given Query.
- getComponentsForQuery(Query) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Returns a Set of independent components that affect the results of the given Query.
- getComponentsForQuery(Query) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Returns a Set of independent components that affect the results of the given Query.
- getComponentsForQuery(Query) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
-
Returns a Set of independent components that affect the results of the given Query.
- getConfig(int) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Return the config Map.
- getConfig(int) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
-
Return the config Map.
- getConfig(int) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return the config Map.
- getConfig(int) - Method in class org.intermine.bio.dataconversion.WormBaseProcessor
-
Return the config Map.
- getConfig(String) - Method in class org.intermine.web.logic.export.http.TableExporterFactory
-
Return the TableExportConfig for the given id.
- getConfigClassDescriptor() - Method in class org.intermine.task.DelimitedFileConfiguration
-
Return the ClassDescriptor of the class to modify.
- getConfigId() - Method in class org.intermine.web.logic.widget.Widget
-
Get the ID of the corresponding WidgetConfig
- getConfiguredTypes() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Get the unqualified class names for which this displayer should be displayed.
- getConnectField() - Method in class org.intermine.api.bag.BagQueryConfig
-
Return the connecting field.
- getConnection() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
-
Get the connection to use when processing.
- getConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Returns a Connection.
- getConnection() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Returns a Connection.
- getConnection() - Method in class org.intermine.sql.Database
-
Gets a Connection to this Database
- getConstrainField() - Method in class org.intermine.api.bag.BagQueryConfig
-
Return the constrain field.
- getConstraint() - Method in class org.intermine.objectstore.query.Query
-
Get the current constraint on this Query
- getConstraint() - Method in interface org.intermine.objectstore.query.Queryable
-
Returns the additional constraint.
- getConstraint() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
-
Returns the additional constraint.
- getConstraint() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
-
Returns the additional constraint.
- getConstraint() - Method in class org.intermine.sql.query.NotConstraint
-
Returns the contained constraint.
- getConstraint() - Method in class org.intermine.template.TemplateValue
-
Returns the constraint that this object was constructed with.
- getConstraintCodes() - Method in class org.intermine.pathquery.PathQuery
-
Return the constraint codes used in the query, some constraint types (subclasses) don't
get assigned a code, these are not included.
- getConstraintDescription(PathConstraint) - Method in class org.intermine.template.TemplateQuery
-
Returns the description attached to the given constraint.
- getConstraintDescriptions() - Method in class org.intermine.template.TemplateQuery
-
Returns the constraint descriptions for this query.
- getConstraintForCode(String) - Method in class org.intermine.pathquery.PathQuery
-
Returns the PathConstraint associated with a given code.
- getConstraintGroups() - Method in class org.intermine.pathquery.PathQuery
-
Returns the outer join constraint codes groups map for this query, if the query verifies
correctly.
- getConstraintLogic() - Static method in class org.intermine.dwr.AjaxServices
-
Get the grouped constraint logic
- getConstraintLogic() - Method in class org.intermine.pathquery.PathQuery
-
Returns the current constraint logic.
- getConstraintLogicForEditableConstraints() - Method in class org.intermine.template.TemplateQuery
-
Return the constraint logic modified to contain only the blocks with editable constraints
- getConstraintLogicForGroup(String) - Method in class org.intermine.pathquery.PathQuery
-
Returns the constraint logic for the given outer join group, if the query verifies correctly.
- getConstraintOp() - Method in class org.intermine.web.logic.template.ConstraintInput
-
Returns constraint operation
- getConstraintPath() - Method in class org.intermine.api.bag.AdditionalConverter
-
- getConstraints() - Method in class org.intermine.objectstore.query.ConstraintSet
-
Returns the Set of constraints.
- getConstraints() - Method in class org.intermine.pathquery.PathQuery
-
Returns a Map of all the constraints in this query, from PathConstraint to the constraint
code used in the constraint logic.
- getConstraints() - Method in class org.intermine.sql.query.ConstraintSet
-
Returns the Set of constraints forming this object.
- getConstraints() - Method in class org.intermine.web.logic.querybuilder.SummaryPath
-
Return summary representations of constraints on this path or an empty list if none exist.
- getConstraints() - Method in class org.intermine.web.logic.template.TemplateResultInput
-
Returns constraints.
- getConstraintsForPath(String) - Method in class org.intermine.pathquery.PathQuery
-
Returns a list of PathConstraints applied to a given path or an empty list.
- getConstraintSwitchOffAbility() - Method in class org.intermine.template.TemplateQuery
-
Returns the constraint SwitchOffAbility for this query.
- getContainsOptions() - Method in class org.intermine.api.query.range.AbstractHelper
-
By default the CONTAINS options are same as the WITHIN options with the left and
right operators swapped.
- getContent(String, boolean, String, String) - Method in class org.intermine.dwr.AjaxServices
-
- getContent() - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig
-
Get the content of the widget.
- getContents() - Method in class org.intermine.api.profile.InterMineBag
-
Returns a List of BagValue (key field value and extra value) of the objects contained
by this bag.
- getContents() - Method in class org.intermine.api.profile.StorableBag
-
Returns a List of BagValue (key field value and extra value) of the objects contained
by this bag.
- getContentsAsIds() - Method in class org.intermine.api.profile.InterMineBag
-
Returns a List which contains the contents of this bag as Integer IDs.
- getContentsOrderByExtraValue() - Method in class org.intermine.api.profile.StorableBag
-
- getContentType() - Method in interface org.intermine.webservice.client.core.Request
-
- getContentType() - Method in class org.intermine.webservice.client.core.RequestImpl
- getContentType() - Method in enum org.intermine.webservice.server.Format
-
- getConversionMapQuery(List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, Object) - Static method in class org.intermine.api.bag.TypeConverter
-
Get conversion query for the types provided, edited so that the first
type is constrained to be in the bag.
- getConversionQuery(List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, Object) - Static method in class org.intermine.api.bag.TypeConverter
-
Get conversion query for the types provided, edited so that the first
type is constrained to be in the bag and the first type is removed from the
view list so that the query only returns the converted type.
- getConversionTemplates() - Method in class org.intermine.api.bag.BagQueryRunner
-
Fetch conversion template queries from the template manager.
- getConversionTemplates(List<ApiTemplate>, Class) - Static method in class org.intermine.api.bag.TypeConverter
-
Return a Map from typeB to a TemplateQuery that will convert from typeA to typeB.
- getConversionTemplates() - Method in class org.intermine.api.template.TemplateManager
-
Return template queries used for converting between types in bag upload and lookup queries,
these are Superuser templates that have been tagged with TagNames.IM_CONVERTER.
- getConvertCountForBag(String, String) - Static method in class org.intermine.dwr.AjaxServices
-
For a given bag name and a type different from the bag type, give the number of
converted objects
- getConvertedObjectIds(Profile, String, List<Integer>, String) - Method in class org.intermine.web.logic.bag.BagConverter
-
- getConvertedObjectMap(List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, Object, ObjectStore) - Static method in class org.intermine.api.bag.TypeConverter
-
Converts a List of objects from one type to another type using a TemplateQuery,
returns a map from an original object to the converted object(s).
- getConvertedObjects(HttpSession, List<ApiTemplate>, Class<? extends InterMineObject>, Class<? extends InterMineObject>, InterMineBag) - Static method in class org.intermine.web.logic.bag.BagConversionHelper
-
Converts a List of objects from one type to another type using a TemplateQuery,
returns the converted objects.
- getConvertedValue(Class<?>) - Method in class org.intermine.objectstore.query.UnknownTypeValue
-
Returns the value, converted (if possible) into the object type given by the input class.
- getCorrection() - Method in interface org.intermine.web.logic.widget.EnrichmentOptions
-
- getCorrection() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
-
- getCorrectionCoefficient() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- getCount() - Method in class org.intermine.api.profile.TagHandler
-
Return a count of the number of tags read.
- getCount() - Method in class org.intermine.api.tracker.track.ListTrack
-
Return the number of items contained into the list
- getCount() - Method in class org.intermine.web.logic.results.ReportInList
-
- getCount() - Method in class org.intermine.web.logic.session.QueryCountQueryMonitor
-
Return the count set with setCount().
- getCount(PathQuery) - Method in class org.intermine.webservice.client.services.QueryService
-
- getCount(String) - Method in class org.intermine.webservice.client.services.QueryService
-
Returns the number of results the specified query will return.
- getCount(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
-
Returns the number of results the specified template will return.
- getCount(TemplateQuery) - Method in class org.intermine.webservice.client.services.TemplateService
-
- getCountItemsWithLengthNotNull() - Method in class org.intermine.api.profile.InterMineBag
-
Return the number of items contained in the bag with length not null
If the type bag is not a subclass of SequenceFeature, return 0
- getCounts(Profile, InterMineBag) - Method in class org.intermine.web.logic.bag.BagConverter
-
Method to return list of values and the counts of converted objects for that object
used for display on list analysis page.
- getCounts() - Method in class org.intermine.web.logic.widget.EnrichmentResults
-
Get the count of each attribute value found in the sample.
- getCreatedAt() - Method in class org.intermine.api.bag.SharingInvite
-
- getCreatedAt() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
-
- getCreatedAt() - Method in class org.intermine.webservice.client.lists.ItemList
-
Get the date when this list was created.
- getCrossReferences() - Method in class org.intermine.bio.dataconversion.UniprotConfig
-
- getCurrentBags(Profile) - Method in class org.intermine.api.bag.BagManager
-
Get the bags this user has access to, as long as they are current.
- getCurrentBagsContainingId(Profile, Integer) - Method in class org.intermine.api.bag.BagManager
-
Fetch the current user or global or shared bags that contain the given id.
- getCurrentBagsOfType(Profile, String) - Method in class org.intermine.api.bag.BagManager
-
Fetch global and user bags current of the specified type or a subclass of the specified type.
- getCurrentFile() - Method in class org.intermine.dataconversion.FileConverter
-
Return the File that is currently being converted.
- getCurrentPage() - Method in class org.intermine.web.tags.table.NavigationBarTag
-
- getCurrentSavedBags() - Method in class org.intermine.api.profile.Profile
-
Get the value of savedBags current
- getCurrentSelectedIdStrings() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Return selected object ids of the current page as a String[], needed for jsp multibox.
- getCurrentSelectedIdStringsList() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Return selected object ids of the current page as a List.
- getCurrentUserBagsOfType(Profile, String) - Method in class org.intermine.api.bag.BagManager
-
Fetch user bags current of the specified type or a subclass of the specified type.
- getCustomConverterCounts(String, String) - Static method in class org.intermine.dwr.AjaxServices
-
For a list and a converter, return types and related counts
- getCvName() - Method in class org.intermine.bio.chado.ChadoCV
-
Return the cvName that was passed to the constructor.
- getCVTermRelationshipResultSet(Connection, String) - Method in class org.intermine.bio.chado.ChadoCVFactory
-
Return the rows from the cvterm_relationship table that relate cvterms from the cv with the
given name.
- getCVTermResultSet(Connection, String) - Method in class org.intermine.bio.chado.ChadoCVFactory
-
Return the rows from the cvterm table that are from the cv with the given name.
- getDAG(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the rows needed to construct the DAG of the data/protocols.
- getData() - Method in class org.intermine.webservice.client.results.RowResultSet
-
- getData() - Method in class org.intermine.webservice.client.results.TabTableResult
-
Get the raw data from this result set.
- getData() - Method in class org.intermine.webservice.client.results.XMLTableResult
-
- getDatabase() - Method in class org.intermine.bio.dataconversion.ChadoProcessor
-
Return the database to read from
- getDatabase() - Method in class org.intermine.dataconversion.DBConverter
-
Get the Database that was passed to the constructor.
- getDatabase() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Returns the Database used by this ObjectStore
- getDatabase(String) - Static method in class org.intermine.sql.DatabaseFactory
-
Returns a connection to the named database
- getDataSet(String, String) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
-
Return a DataSet item with the given details.
- getDataSet(String, String) - Method in class org.intermine.bio.dataconversion.BioFileConverter
-
Return a DataSet ref with the given details.
- getDataSet() - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
Return the DataSet to add to each object.
- getDataSet() - Method in class org.intermine.bio.dataconversion.GFF3Converter
-
Return the DataSet Item created for this GFF3Converter from the data set title passed
to the constructor.
- getDataSetItem(int) - Method in class org.intermine.bio.dataconversion.BioDBConverter
-
Return the DataSet Item created from the dataSetTitle.
- getDataSetItem(String, Item) - Method in class org.intermine.bio.dataconversion.BioDBConverter
-
Return a DataSource item for the given name
- getDataSetItem(String, String, String, Item) - Method in class org.intermine.bio.dataconversion.BioDBConverter
-
Return a DataSource item with the given details.
- getDataSetItem(int) - Method in class org.intermine.bio.dataconversion.GenomeDBConverter
-
Return the DataSet Item created from the dataSetTitle.
- getDataSetItem(String, String, String, Item) - Method in class org.intermine.bio.dataconversion.GFF3Converter
-
Return a DataSource item with the given details.
- getDataSetReferenceList() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Return a ReferenceList containing the DataSet Items ids set by addDataSet()
- getDatasetRefId() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getDataSetTitle(int) - Method in class org.intermine.bio.dataconversion.BioDBConverter
-
Return the DataSet title for a given taxon id.
- getDataSetTitle(int) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
-
Default implementation that makes a data set title based on the data source name.
- getDataSetTitle(int) - Method in class org.intermine.bio.dataconversion.GenomeDBConverter
-
Default implementation that makes a data set title based on the data source name.
- getDataSource(String) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
-
Return a DataSource item for the given title
- getDataSource(String) - Method in class org.intermine.bio.dataconversion.BioFileConverter
-
Return a DataSource item for the given title
- getDataSource() - Method in class org.intermine.bio.dataconversion.GFF3Converter
-
Return the DataSource Item created for this GFF3Converter from the data source name passed
to the constructor.
- getDataSource() - Method in class org.intermine.sql.Database
-
Gets the DataSource object for this Database
- getDataSourceItem() - Method in class org.intermine.bio.dataconversion.BioDBConverter
-
Return the DataSource Item created from the dataSourceName.
- getDataSourceItem(String) - Method in class org.intermine.bio.dataconversion.BioDBConverter
-
Return a DataSet item for the given title
- getDataSourceItem(String) - Method in class org.intermine.bio.dataconversion.GFF3Converter
-
Return a DataSet item for the given title
- getDataSourceName() - Method in class org.intermine.bio.dataconversion.BioDBConverter
-
Return the data source name set by setDataSourceName().
- getDataTracker() - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
-
Returns the data tracker being used.
- getDateCreated() - Method in class org.intermine.api.profile.InterMineBag
-
Return the creation date that was passed to the constructor.
- getDateCreated() - Method in class org.intermine.api.profile.InvalidBag
-
- getDateCreated() - Method in class org.intermine.api.profile.SavedQuery
-
Get the date on which the query was created.
- getDateCreated() - Method in class org.intermine.api.profile.StorableBag
-
Get the date that this bag was created at.
- getDayToken() - Method in class org.intermine.api.profile.Profile
-
Get a token with at least an hour of validity, and up to 24 hours.
- getDayToken() - Method in class org.intermine.api.util.AnonProfile
-
- getDb() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- getDbDescription() - Method in class org.intermine.bio.util.ClobAccessReverseComplement
-
Returns a String that describes this object sufficiently for it to be recreated given an
ObjectStore.
- getDbDescription() - Method in class org.intermine.objectstore.query.ClobAccess
-
Returns a String that describes this object sufficiently for it to be recreated given an
ObjectStore.
- getDbDescription() - Method in class org.intermine.objectstore.query.PendingClob
-
Returns a String that describes this object sufficiently for it to be recreated given an
ObjectStore.
- getDbref() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getDbrefs() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getDbxrefResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return the interesting rows from the dbxref table.
- getDbxrefs() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the first value of the Dbxref field from the attributes of this record.
- getDefaultClass() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
-
Returns the QueryClass that represents the collection in this object.
- getDefaultClass() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
-
Returns the QueryClass that represents the collection in this object.
- getDefaultEventIndex() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
-
- getDefaultEventIndex() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
-
- getDefaultFileName() - Method in class org.intermine.webservice.server.query.CodeService
-
- getDefaultFileName() - Method in class org.intermine.webservice.server.query.QueryRetrieverService
-
- getDefaultFileName() - Method in class org.intermine.webservice.server.SchemaListService
-
- getDefaultFileName() - Method in class org.intermine.webservice.server.SummaryService
-
- getDefaultFileName() - Method in class org.intermine.webservice.server.WebService
-
- getDefaultFilterValue(WidgetConfig, InterMineBag) - Method in class org.intermine.webservice.server.widget.WidgetService
-
Get the default filter value for a widget.
- getDefaultFormat() - Method in class org.intermine.webservice.server.core.JSONService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.lists.AvailableListsService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.lists.ListMakerService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.model.ModelService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.path.PossibleValuesService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.query.CodeService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.query.QueryRetrieverService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.query.QueryToListService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.query.QueryUploadService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.query.result.QueryResultService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.query.result.TableRowService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.template.AvailableTemplatesService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.user.DeregistrationService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.VersionService
-
- getDefaultFormat() - Method in class org.intermine.webservice.server.WebService
-
- getDefaultOperator(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Get the default operator to apply to new constraints.
- getDefaultOutput(PrintWriter, OutputStream, String) - Method in class org.intermine.webservice.server.WebService
-
Make the default output for this service.
- getDefaultOutput(PrintWriter, OutputStream) - Method in class org.intermine.webservice.server.WebService
-
Make the default output for this service.
- getDefaultPermission(Profile) - Static method in class org.intermine.api.profile.ProfileManager
-
Wrap a profile in the default permission level.
- getDefaultPropertyIndex() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
-
- getDefaultPropertyIndex() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
-
- getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
-
Returns default style class.
- getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureBodyTag
-
Returns default style class.
- getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureDetailsTag
-
Returns default style class.
- getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureHeadTag
-
Returns default style class.
- getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
-
Returns default style class.
- getDefaultStyleClass() - Method in class org.intermine.web.tags.disclosure.DisclosureTitleTag
-
Returns default style class.
- getDefaultValue() - Method in class org.intermine.api.mines.LocalMine
-
- getDefaultValue() - Method in interface org.intermine.api.mines.Mine
-
get first default value. used in querybuilder to select default extra value
- getDefaultValue() - Method in class org.intermine.api.mines.RemoteMine
-
- getDefaultValues() - Method in class org.intermine.api.mines.LocalMine
-
- getDefaultValues() - Method in interface org.intermine.api.mines.Mine
-
- getDefaultValues() - Method in class org.intermine.api.mines.RemoteMine
-
- getDefaultViewForClass(String, Model, WebConfig, String) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
-
Return a list of string paths that are defined as WebConfig to be shown in results.
- getDefaultViewForClass(String, Model, WebConfig) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
-
Return a list of string paths that are defined as WebConfig to be shown in results.
- getDeleted(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return deleted subs in the chado db.
- getDeletedClasses() - Method in class org.intermine.api.profile.ModelUpdate
-
Return a set containing all the deleted classes
- getDeletionLocationResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Return a result set containing location for deletions (chromosome_structure_variation)
objects.
- getDescr() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- getDescription() - Method in class org.intermine.api.mines.LocalMine
-
- getDescription() - Method in interface org.intermine.api.mines.Mine
-
- getDescription() - Method in class org.intermine.api.mines.RemoteMine
-
- getDescription() - Method in class org.intermine.api.profile.InterMineBag
-
Return the description of this bag.
- getDescription() - Method in class org.intermine.api.profile.InvalidBag
-
- getDescription() - Method in class org.intermine.api.profile.StorableBag
-
- getDescription() - Method in interface org.intermine.api.search.WebSearchable
-
Return the description of this object.
- getDescription() - Method in class org.intermine.bio.ontology.OboTerm
-
Get the term description.
- getDescription(String) - Method in class org.intermine.pathquery.PathQuery
-
Returns the description for a given path, or null if no description is registered.
- getDescription() - Method in class org.intermine.pathquery.PathQuery
-
Gets the description for this PathQuery.
- getDescription() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Return the label associated with a constraint if editing a template query constraint.
- getDescription() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
-
Get the description for a constraint.
- getDescription() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- getDescription() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
-
Get the description
- getDescription() - Method in class org.intermine.web.struts.TemplateSettingsForm
-
Return the description.
- getDescription() - Method in class org.intermine.webservice.client.lists.ItemList
-
- getDescription() - Method in class org.intermine.webservice.client.widget.Widget
-
- getDescription() - Method in class org.intermine.webservice.server.lists.ListInput
-
- getDescription(int) - Static method in class org.intermine.webservice.server.StatusDictionary
-
- getDescriptions() - Method in class org.intermine.pathquery.PathQuery
-
Returns an unmodifiable Map which is a copy of the current set of path descriptions of this
query at the time of execution of this method.
- getDescriptiveString() - Method in class org.intermine.pathquery.PathConstraintLoop
-
Returns a descriptive string for this constraint, mainly useful for checking uniqueness.
- getDescriptor() - Method in class org.intermine.web.logic.results.DisplayCollection
-
Get ReferenceDescriptor for this reference.
- getDescriptor() - Method in class org.intermine.web.logic.results.DisplayReference
-
Get ReferenceDescriptor for this reference.
- getDescriptor() - Method in class org.intermine.web.logic.results.InlineList
-
- getDescriptors(Model) - Static method in class org.intermine.dataloader.DataLoaderHelper
-
Build a map from class and field names to a priority-ordered List of source name Strings.
- getDirectChildren() - Method in class org.intermine.bio.chado.ChadoCVTerm
-
Get the direct children of this term.
- getDirectDataLoader() - Method in class org.intermine.task.DirectDataLoaderTask
-
Return the DirectDataLoader for this Task.
- getDirection() - Method in class org.intermine.pathquery.OrderElement
-
Returns the order direction of this OrderElement.
- getDirectParents() - Method in class org.intermine.bio.chado.ChadoCVTerm
-
Get the direct parents of this term.
- getDisableResultsCache() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Gets the disableResultsCache configuration option.
- getDisableResultsCache() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Gets the disableResultsCache configuration option.
- getDisplayer() - Method in class org.intermine.web.logic.config.FieldConfig
-
Get the displayer for that field
- getDisplayerName() - Method in class org.intermine.web.displayer.ReportDisplayer
-
Gimme my name
- getDisplayerPage() - Method in class org.intermine.web.logic.results.ReportObjectField
-
Return path to a custom displayer
- getDisplayFields() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
- getDisplayName() - Method in class org.intermine.web.logic.config.FieldConfig
-
Get the label to display in the webapp for this field.
- getDisplayName() - Method in class org.intermine.web.logic.config.Type
-
- getDisplayName() - Method in class org.intermine.web.logic.results.ReportObjectField
-
Get the label to display in the webapp for this field.
- getDisplaySummary(PathQuery) - Static method in class org.intermine.web.logic.querybuilder.QueryBuilderSummaryHelper
-
Create summary information of the paths currently in a query and their constraints for
display in the QueryBuilder summary section.
- getDocument() - Method in class org.intermine.api.lucene.KeywordSearchHit
-
document
- getDoesntContainOptions() - Method in class org.intermine.api.query.range.AbstractHelper
-
By default the DOES NOT CONTAINS options are negation of the CONTAINS options.
- getDoesntOverlapOptions() - Method in class org.intermine.api.query.range.AbstractHelper
-
By default the DOES NOT OVERLAP options are negation of the OVERLAPS options.
- getDoGzip() - Method in class org.intermine.web.struts.TableExportForm
-
Get whether the output should be GZIPped.
- getDomain() - Method in class org.intermine.api.beans.PartnerLink
-
- getDomain() - Method in class org.intermine.api.mines.ObjectRequest
-
- getDomainLabel() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
Get the domainLabel
- getDoneAlready() - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
-
Returns the doneAlready Set, for logging purposes
- getDoNotTruncate() - Method in class org.intermine.web.logic.config.FieldConfig
-
Return the value of the doNotTruncate flag.
- getDoNotTruncate() - Method in class org.intermine.web.logic.results.ReportObjectField
-
- getDouble(String) - Method in class org.intermine.webservice.client.results.Item
-
Get a property known to be a double.
- getDriver() - Method in class org.intermine.sql.Database
-
Gets the driver this Database
- getECNumbers() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- geteditable() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- getEditableConstraints(String) - Method in class org.intermine.template.TemplateQuery
-
For a path with editable constraints, get all the editable constraints as a List, or the
empty list if there are no editable constraints on that path.
- getEditableConstraints() - Method in class org.intermine.template.TemplateQuery
-
Returns the list of all editable constraints.
- getEditablePaths() - Method in class org.intermine.template.TemplateQuery
-
Get the paths of all editable constraints in this template.
- getEditingConstraintCode() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Get the constraint that is being edited or null if creating a new constraint.
- getEditingView(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Get the view list that the user is currently editing.
- getEFactors(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the rows needed for the experimental factors.
- getEffectiveOrderBy() - Method in class org.intermine.objectstore.query.Query
-
Gets the effective ORDER BY clause of this Query, such as may be used to create SQL.
- getEffectiveView() - Method in class org.intermine.webservice.server.core.TableRowIterator
-
- getElementClassDescriptors() - Method in class org.intermine.pathquery.Path
-
Return a List of the ClassDescriptor objects for each element of the path.
- getElementId() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
-
Return the table identifier if isTable==true.
- getElements() - Method in class org.intermine.pathquery.Path
-
Return a list of field names, one per path element (except for the first, which is a
class).
- getElementsContainingField(String, String) - Method in class org.intermine.pathquery.Path
-
Return the indexes of elements containing the field given in input
- getElementType(String) - Method in interface org.intermine.model.InterMineObject
-
Returns the element type of a collection by name.
- getElementType(String) - Method in class org.intermine.objectstore.proxy.ProxyReference
-
Returns the element type of a collection by name.
- getEmail() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
-
- getEmail() - Method in class org.intermine.webservice.server.JWTVerifier.Verification
-
- getEmailAddress() - Method in class org.intermine.api.profile.Profile
-
Get this user's preferred email address.
- getEmailer(Properties) - Static method in class org.intermine.web.context.EmailerFactory
-
- getEncodedUrl() - Method in interface org.intermine.webservice.client.core.Request
-
- getEncodedUrl() - Method in class org.intermine.webservice.client.core.RequestImpl
-
- getEnd() - Method in interface org.intermine.api.query.range.Range
-
- getEnd() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the end field of this record.
- getEnd() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
-
Get start value
- getEnd() - Method in class org.intermine.objectstore.query.OverlapRange
-
Returns the right parameter.
- getEnd() - Method in class org.intermine.webservice.server.core.Page
-
- getEndClassDescriptor() - Method in class org.intermine.pathquery.Path
-
If the last element in the path is a reference or collection return the ClassDescriptor that
the reference or collection references.
- getEndClassName() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
- getEndFieldDescriptor() - Method in class org.intermine.pathquery.Path
-
Return the FieldDescriptor of the last element in the path or null if the path has just one
element.
- getEndRow() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Get the index of the last row of this page
- getEndType() - Method in class org.intermine.pathquery.Path
-
Return the type of the last element in the path, regardless of whether it is an attribute
or a class.
- getEnrich() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
The enrich property is the path to the value that should be enriched.
- getEnrichIdentifier() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- getEnrichmentWidgets() - Method in class org.intermine.webservice.client.services.WidgetService
-
- getEnsemblIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a Ensembl gene id resolver
- getEnsemblIdResolver(boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a Ensembl gene resolver
- getEnsemblPrefix() - Method in class org.intermine.bio.util.OrganismData
-
- getEof() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Get the equivalent object fetcher.
- getEquivalentObjects(InterMineObject, Source) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Returns a Set of objects from the idMap or database that are equivalent to the given
object, according to the primary keys defined by the given Source.
- getEquivalentsFor(List<ResultsRow<Object>>) - Method in class org.intermine.dataloader.BatchingFetcher
-
Fetches the equivalent object information for a whole batch of objects.
- getEquivalentsForObjects(List<FastPathObject>) - Method in class org.intermine.dataloader.BatchingFetcher
-
Fetches the equivalent object information for a whole batch of objects.
- getError() - Method in interface org.intermine.api.idresolution.Job
-
- getError() - Method in class org.intermine.api.idresolution.ResolutionJob
-
- getError() - Method in class org.intermine.api.idresolution.UpgradeJob
-
- getError() - Method in class org.intermine.webservice.server.output.Output
-
Gets the error message.
- getError() - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
-
- getErrorCorrection() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
which method of errorcorrection the user chose.
- getErrorCorrection() - Method in class org.intermine.web.struts.WidgetForm
-
- getErrorElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
-
- getErrorElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
-
- getErrorOnInitialiser(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Gets the blocking error codes from the servlet context.
- getErrors() - Method in class org.intermine.webservice.server.query.result.XMLValidator
-
Returns errors occurred during parsing xml.
- getErrors() - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
-
Returns errors occurred during parsing xml.
- getErrorsAndWarnings() - Method in class org.intermine.webservice.server.query.result.XMLValidator
-
Returns errors and warning occurred during parsing xml.
- getEscapeXml() - Method in class org.intermine.web.logic.config.FieldConfig
-
Return the value of the escapeXml flag.
- getEscapeXml() - Method in class org.intermine.web.logic.results.ReportObjectField
-
- getEstimatedRows() - Method in class org.intermine.sql.query.ExplainResult
-
Returns the best current estimate for the number of rows for this query.
- getEstimatedSize() - Method in class org.intermine.api.results.WebResults
-
Get the estimated number of rows of this table
- getEstimatedSize() - Method in interface org.intermine.api.results.WebTable
-
Get the estimated number of rows of this table
- getEstimatedSize() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Get the (possibly estimated) number of resultElementRows of this table
- getEvaluables() - Method in class org.intermine.objectstore.query.MultipleInBagConstraint
-
Returns the evaluables that this object was constructed with.
- getEvent() - Method in class org.intermine.api.tracker.track.ListTrack
-
Return the type of event to track (creation or list execution )
- getEventSetDescriptors() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
-
- getEventSetDescriptors() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
-
- getExactSize() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Get the exact number of resultElementRows of this table
- getException() - Method in class org.intermine.api.lucene.InterMineObjectFetcher
-
Get the error that occurred during processing, if any.
- getExcludeList() - Method in class org.intermine.task.ConverterTask
-
Return the list set by setExcludeList().
- getExistingBagName() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
-
Gets the value of existingBagName
- getExistingBagName() - Method in class org.intermine.web.struts.SaveBagForm
-
Gets the value of existingBagName
- getExistingLoops() - Method in class org.intermine.pathquery.PathQuery
-
Returns the set of loop constraint descriptive strings, for the purpose of checking for
uniqueness.
- getExperimentProperties(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the rows needed for submission from the experiment_prop table.
- getExperimentTitles(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the rows needed for experiment from the experiment_prop table.
- getExpiry() - Method in class org.intermine.webservice.server.user.DeletionToken
-
- getExplain() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
-
Returns the ExplainResult of this Candidate, fetching the data if not already present.
- getExplainResult(Query) - Method in class org.intermine.sql.precompute.BestQueryExplainer
-
Internal method that creates an ExplainResult.
- getExplainResult(String) - Method in class org.intermine.sql.precompute.BestQueryExplainer
-
Internal method that creates an ExplainResult.
- getExplainResult(Query) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose
-
Internal method that creates an ExplainResult.
- getExplainResult(String) - Method in class org.intermine.sql.precompute.BestQueryExplainerVerbose
-
Internal method that creates an ExplainResult.
- getExplainText() - Method in class org.intermine.sql.query.PostgresExplainResult
-
Returns the text of the explain result, in human readable form.
- getExporter(OutputStream, String, List<String>) - Method in class org.intermine.web.logic.export.http.CSVHttpExporter
-
Do the export.
- getExporter(OutputStream, String, List<String>) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
-
Do the export.
- getExporter(OutputStream, String, List<String>) - Method in class org.intermine.web.logic.export.http.TabHttpExporter
-
Do the export.
- getExporter(String) - Method in class org.intermine.web.logic.export.http.TableExporterFactory
-
Return the exporter class for the given id.
- getExportField() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
- getExportQuery(List<String>) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
-
- getExportResults(String[]) - Method in class org.intermine.web.logic.widget.EnrichmentWidget
-
- getExportResults(String[]) - Method in class org.intermine.web.logic.widget.GraphWidget
- getExportResults(String[]) - Method in class org.intermine.web.logic.widget.HTMLWidget
-
- getExportResults(String[]) - Method in class org.intermine.web.logic.widget.TableWidget
- getExportResults(String[]) - Method in class org.intermine.web.logic.widget.TableWidgetLdr
-
- getExportResults(String[]) - Method in class org.intermine.web.logic.widget.Widget
-
- getExporttype() - Method in class org.intermine.web.struts.WidgetForm
-
- getExtension() - Method in class org.intermine.webservice.server.query.CodeService
-
- getExtension() - Method in class org.intermine.webservice.server.WebService
-
- getExternalLink() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- getExternalLink() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
- getExternalLink() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- getExternalLinkLabel() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
- getExtra() - Method in class org.intermine.api.profile.BagValue
-
- getExtraAttribute() - Method in class org.intermine.web.logic.widget.PopulationInfo
-
- getExtraAttribute() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
-
- getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
- getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig
-
- getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
Do-nothing implementation of superclass method
- getExtraAttributes(InterMineBag, ObjectStore) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- getExtraAttributes(ObjectStore, InterMineBag) - Method in interface org.intermine.web.logic.widget.WidgetHelper
-
Get the extra attributes needed for the DataSetLoader
- getExtraConnectFieldPath() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
- getExtraConstraintClassName() - Method in class org.intermine.api.bag.BagQueryConfig
-
Return the class name that was passed to the constructor.
- getExtraConstraintClassName() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
If a LOOKUP constraint and an extra value constraint is available return the classname of
the extra constraint so it can be displayed.
- getExtraConstraintValues() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
If a LOOKUP constraint and an extra constraint is available for this path, return a list of
the possible values for populating a dropdown.
- getExtraCorrectionCoefficient() - Method in interface org.intermine.web.logic.widget.EnrichmentOptions
-
- getExtraCorrectionCoefficient() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
-
- getExtraCorrectionCoefficient() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
-
- getExtraFeatureConstraint() - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Return an extra constraint to be used when querying the feature table.
- getExtraFeatureConstraint() - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
-
Return an extra constraint to be used when querying the feature table.
- getExtraFeatureConstraint() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return an extra constraint to be used when querying the feature table.
- getExtraFieldValue() - Method in class org.intermine.web.struts.BagUploadConfirmForm
-
Set the extra field value - the optional constraint on the bag upload page
- getExtraFieldValue() - Method in class org.intermine.web.struts.BuildBagForm
-
Get the value to use when creating an extra constraint on a BagQuery, configured in
BagQueryConfig.
- getExtraFieldValue() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
-
- getExtraParams() - Method in class org.intermine.web.struts.TableExportForm
-
Extra parameters map for use by sub classes.
- getExtraValue() - Method in interface org.intermine.api.idresolution.JobInput
-
- getExtraValue(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
-
A static method for getting the extra-value if there is one, or
null if there is none to be got.
- getExtraValue() - Method in class org.intermine.pathquery.PathConstraintLookup
-
Returns the extra value for this constraint.
- getExtraValue() - Method in class org.intermine.template.TemplateValue
-
- getExtraValue() - Method in class org.intermine.web.logic.bag.WebJobInput
-
- getExtraValue() - Method in class org.intermine.web.logic.template.ConstraintInput
-
Returns extra value.
- getExtraValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Gets the value of extraValue
- getExtraValue() - Method in class org.intermine.webservice.client.template.TemplateParameter
-
- getExtraValue() - Method in class org.intermine.webservice.server.lists.ListInput
-
- getExtraValue() - Method in class org.intermine.webservice.server.lists.ListsServiceInput
-
- getExtraValueFieldClass() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
- getExtraValues() - Method in class org.intermine.web.struts.TemplateForm
-
Get the extra values
- getExtraValues(String) - Method in class org.intermine.web.struts.TemplateForm
-
Get an extra value
- getFacets() - Static method in class org.intermine.api.lucene.KeywordSearch
-
get list of facet fields and names
- getFacets() - Method in class org.intermine.api.lucene.ResultsWithFacets
-
- getFactory() - Static method in class org.intermine.bio.util.ClobAccessReverseComplement
-
Returns a ClobAccessSubclassFactory object that will access the constructor of this class
quickly, in order to avoid using reflection for every clob.
- getFactory() - Method in class org.intermine.webservice.client.core.Service
-
Get the ServiceFactory this service was constructed with.
- getFastList(String, String, int) - Method in class org.intermine.web.autocompletion.AutoCompleter
-
Returns n search results
- getFeature() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Return the feature Item set by setFeature()
- getFeature() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
used to get the feature to store.
- getFeatureCVTermResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return the interesting rows from the feature_cvterm/cvterm table.
- getFeatureIdQuery() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return an SQL query that finds the feature_ids of all rows from the feature table that we
need to process.
- getFeatureLocResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return the interesting rows from the featureloc table.
- getFeatureMap() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Fetch the populated map of chado feature id to FeatureData objects.
- getFeaturePropResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return the interesting rows from the featureprop table.
- getFeatureRelationshipResultSet(Connection, boolean) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return the interesting rows from the feature_relationship table.
- getFeatures() - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Get a list of the chado/so types of the LocatedSequenceFeatures we wish to load.
- getFeatures() - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
-
Get a list of the chado/so types of the LocatedSequenceFeatures we wish to load.
- getFeatures() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Get a list of the chado/so types of the SequenceFeatures we wish to load.
- getFeatures() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getFeatures() - Method in class org.intermine.bio.dataconversion.WormBaseProcessor
-
Get a list of the chado/so types of the LocatedSequenceFeatures we wish to load.
- getFeatureTableResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return the interesting rows from the features table.
- getFeatureTypes() - Method in class org.intermine.bio.dataconversion.UniprotConfig
-
if NULL, all feature types will be loaded.
- getField() - Method in class org.intermine.api.lucene.KeywordSearchFacet
-
internal field name
- getField() - Method in class org.intermine.api.lucene.KeywordSearchFacetData
-
get single/first field or null
- getField() - Method in interface org.intermine.api.results.ResultCell
-
- getField() - Method in class org.intermine.api.results.ResultElement
-
Get the field value
- getField() - Method in class org.intermine.webservice.server.core.TableCell
-
- getFieldConfig(WebConfig, FieldDescriptor) - Static method in class org.intermine.web.logic.config.FieldConfigHelper
-
Get a field config object for a particular descriptor.
- getFieldConfig(WebConfig, ClassDescriptor, FieldDescriptor) - Static method in class org.intermine.web.logic.config.FieldConfigHelper
-
Get a field config object for a particular descriptor.
- getFieldConfig(String) - Method in class org.intermine.web.logic.config.Type
-
Return a FieldConfig for a particular field if it has been specified, otherwise return null
- getFieldConfig(String, String) - Method in class org.intermine.web.logic.config.WebConfig
-
Return the FieldConfig for a particular field of the specified field, or null if field not
configured.
- getFieldConfig() - Method in class org.intermine.web.logic.results.InlineTableResultElement
-
- getFieldConfigMap() - Method in class org.intermine.web.logic.config.Type
-
Return a Map from FieldConfig.fieldName to FieldConfig objects.
- getFieldConfigs() - Method in class org.intermine.web.logic.config.Type
-
Get the List of FieldConfig objects
- getFieldConfigs(String) - Method in class org.intermine.web.logic.config.WebConfig
-
Return a FieldConfigs for a particular class or an empty list if no config is defined.
- getFieldConfigs() - Method in class org.intermine.web.logic.results.ReportObject
-
Return a list of field configs
- getFieldConfigs() - Method in class org.intermine.web.search.KeywordSearchResult
-
fieldConfigs
- getFieldDescriptor() - Method in class org.intermine.pathquery.Node
-
- getFieldDescriptor() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
-
Return the last field descriptor (the last element) of the path.
- getFieldDescriptor() - Method in class org.intermine.web.logic.results.InlineResultsTable
-
Get the fields descriptor this list represents.
- getFieldDisplayName(String) - Method in class org.intermine.web.logic.results.ReportObject
-
Return a string to display as the name of a field.
- getFieldExporter() - Method in class org.intermine.web.logic.config.FieldConfig
-
Return the class name of the FieldExporter to use when this field is viewed.
- getFieldExpr() - Method in class org.intermine.web.logic.config.FieldConfig
-
Return the JSTL expression for the object.
- getFieldName() - Method in class org.intermine.bio.chado.config.CreateCollectionAction
-
Return the fieldName that was passed to the constructor.
- getFieldName() - Method in class org.intermine.bio.chado.config.SetFieldConfigAction
-
Return the field name that was passed to the constructor.
- getFieldName() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
-
Returns the name of the field.
- getFieldName() - Method in class org.intermine.objectstore.query.QueryField
-
Returns the name of the field.
- getFieldName() - Method in class org.intermine.objectstore.query.QueryForeignKey
-
Gets the fieldname of this QueryReference.
- getFieldName() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
-
Returns the name of the field.
- getFieldName() - Method in class org.intermine.objectstore.query.QueryReference
-
Gets the fieldname of this QueryReference.
- getFieldName() - Method in class org.intermine.pathquery.Node
-
Gets the value of fieldName
- getFieldName(int) - Method in class org.intermine.web.autocompletion.LuceneObjectClass
-
return the fieldName at position index
- getFieldName() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
-
Returns the fieldname for this path.
- getFieldNames() - Method in class org.intermine.api.lucene.InterMineObjectFetcher
-
get list of fields contained in the fetched documents
- getFieldNames() - Method in class org.intermine.web.autocompletion.LuceneObjectClass
-
getFieldNames
- getFieldNumber() - Method in class org.intermine.objectstore.query.PathExpressionField
-
Returns the field number.
- getFieldProxy(String) - Method in class org.intermine.objectstore.proxy.ProxyReference
- getFields() - Method in class org.intermine.api.lucene.KeywordSearchFacetData
-
array of field names, only used for path right now
- getFieldToAlias(FromElement) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- getFieldType(String) - Method in class org.intermine.objectstore.proxy.ProxyReference
- getFieldValue(String) - Method in class org.intermine.objectstore.proxy.ProxyReference
- getFieldValue(String) - Method in class org.intermine.web.logic.results.ReportObject
-
Get field value for a field name (expression)
- getFieldValues(String, String) - Method in class org.intermine.objectstore.ObjectStoreSummary
-
Get a list of the possible values (as Strings) for a given field in a given class.
- getFieldValues() - Method in class org.intermine.web.search.KeywordSearchResult
-
values of all fields
- getFieldValues(ObjectStore, ObjectStoreSummary, String, String) - Static method in class org.intermine.web.struts.BagBuildController
-
Return a list of the possible field values for the given class/field name combination.
- getFileName() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
-
Returns the filename that should be associated with this query.
- getFilename(String, String) - Static method in class org.intermine.modelproduction.MetadataManager
-
Given a key and model name, return filename for reading/writing.
- getFilter() - Method in interface org.intermine.web.logic.widget.WidgetOptions
-
- getFilter() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
filter values get used in the query to constrain the results in some way, and they can be
changed by the user.
- getFilter() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
-
- getFilterLabel() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- getFilterLabel() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
the label for the filter.
- getFilters() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- getFilters() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
filter values get used in the query to constrain the results in some way, and they can be
changed by the user.
- getFilters() - Method in class org.intermine.webservice.client.widget.Widget
-
- getFiltersValues(ObjectStore, InterMineBag) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- getFilterWebSearchables(HttpServletRequest, String, String, String) - Static method in class org.intermine.web.struts.WebSearchableListController
-
Get all the WebSearchables in the given scope and of the given type.
- getFinalItems() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Return items that need extra processing that can only be done after all other GFF features
have been read.
- getFirstAlias() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the first value of the Alias field from the attributes of this record.
- getFirstColumnForClass(PagedTable, Class<?>) - Static method in class org.intermine.web.logic.export.ExportHelper
-
Find the first column index for the specified class or a subclass in the
page table (may be a parent class of a field being displayed).
- getFirstOrderByHasNoNulls() - Method in class org.intermine.sql.precompute.PrecomputedTable
-
Returns true if the first element of the ORDER BY clause is a column that contains no nulls.
- getFirstSelectedFields(ObjectStore, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Return the fields for the first selected objects.
- getFishIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a fish id resolver
- getFishIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a fish id resolver
- getFishIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a fish id resolver
- getFixedOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
If a dropdown is available for a constraint fewer operations are possible, return the list
of operations.
- getFlatSelect() - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
-
Converts a SELECT list from a normal query into a representation of the columns returned
in this converted list.
- getFlattenedResults() - Method in class org.intermine.web.logic.widget.TableWidget
-
Get the flattened results
- getFlattenedResults() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
-
get the flattened results
- getFloat(String) - Method in class org.intermine.webservice.client.results.Item
-
Get a property known to be an float.
- getFlyBaseMiscCV(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Get ChadoCV object representing the FlyBase misc cv.
- getFlyBaseSequenceOntologyCV(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Get ChadoCV object representing SO from FlyBase.
- getFlyIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a fly id resolver
- getFlyIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a fly id resolver
- getFlyIdResolver(Set<String>) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a fly id resolver
- getFlyIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a fly id resolver
- getFlyIdResolver(Set<String>, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a fly id resolver
- getFooter() - Static method in class org.intermine.xml.full.FullRenderer
-
Return the Full XML file footer
- getFormat() - Method in enum org.intermine.api.mines.ContentType
-
- getFormat() - Method in class org.intermine.web.struts.CSVExportForm
-
Return the format field ("csv", "tab", ...)
- getFormat() - Method in class org.intermine.webservice.server.WebService
-
Returns required output format.
- getFormatted() - Method in class org.intermine.web.logic.results.ReportObject.TitleValue
-
Get the formatted version, with e.g. italics tags.
- getFormattedClassName() - Method in class org.intermine.web.logic.config.Type
-
- getFormattedClassName(String) - Static method in class org.intermine.web.logic.config.Type
-
- getFormattedName() - Method in class org.intermine.web.logic.config.FieldConfig
-
- getFormattedName(String) - Static method in class org.intermine.web.logic.config.FieldConfig
-
- getFormattedTrack() - Method in class org.intermine.api.tracker.track.KeySearchTrack
-
- getFormattedTrack() - Method in class org.intermine.api.tracker.track.ListTrack
-
Return the track formatted into an array of String to be saved in the database
- getFormattedTrack() - Method in class org.intermine.api.tracker.track.LoginTrack
-
Return the track formatted into an array of String to be saved in the database
- getFormattedTrack() - Method in class org.intermine.api.tracker.track.QueryTrack
-
- getFormattedTrack() - Method in class org.intermine.api.tracker.track.TemplateTrack
-
Return the track formatted into an array of String to be saved in the database
- getFormattedTrack() - Method in interface org.intermine.api.tracker.track.Track
-
Return the track formatted into an array of String to be saved in the database
- getFormatter() - Static method in class org.intermine.webservice.server.core.ISO8601DateFormat
-
- getFormFile() - Method in class org.intermine.web.struts.BuildBagForm
-
Get the FormFile.
- getFormFile() - Method in class org.intermine.web.struts.ImportXMLForm
-
Get the FormFile.
- getFragmentFromURI(String) - Static method in class org.intermine.util.XmlUtil
-
Return the fragment portion of a URI string (i.e. everything after a #).
- getFriendlyDesc(Object) - Static method in class org.intermine.util.DynamicUtil
-
Creates a friendly description of an object - that is, the class and the ID (if it has one).
- getFriendlyMineLinks(String, String, String) - Static method in class org.intermine.dwr.AjaxServices
-
used on REPORT page
For a gene, generate links to other intermines.
- getFriendlyMines() - Method in class org.intermine.api.mines.FriendlyMineManager
-
Return a list of Mines listed in config.
- getFriendlyName() - Method in class org.intermine.pathquery.Node
-
Gets a friendly name for display on the web site.
- getFriendlyName() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
-
Returns the last element of the path.
- getFrom() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- getFrom() - Method in class org.intermine.objectstore.query.Query
-
Returns all FromElements in the FROM clause
- getFrom() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
-
Returns the additional FROM list.
- getFrom() - Method in class org.intermine.sql.query.Query
-
Gets the Set of from tables for this query.
- getFromElement() - Method in class org.intermine.objectstore.query.QueryField
-
Gets the FromElement of which the field is a member
- getFrontcolor() - Method in class org.intermine.api.mines.LocalMine
-
- getFrontcolor() - Method in interface org.intermine.api.mines.Mine
-
- getFrontcolor() - Method in class org.intermine.api.mines.RemoteMine
-
- getFullName(String) - Static method in class org.intermine.webservice.server.CodeTranslator
-
Returns corresponding fullName of translated operation.
- getGap() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the first value of the Gap field from the attributes of this record.
- getGeneDesignation() - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
-
Where to get the gene identifier from. e.g. in WormBase, it's the gene ID.
- getGeneDesignation(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig
-
A string value, e.g.
- getGeneDesignation(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getGeneIdentifierFields(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig
-
- getGeneInfoRecords() - Method in class org.intermine.bio.dataconversion.NcbiGeneInfoParser
-
Return information read from the file, for each taxon id there is one GeneInfoRecord per row
in the file.
- getGeneNames() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getGeneratedPathDescription(String) - Method in class org.intermine.pathquery.PathQuery
-
Returns the path description for the given path.
- getGenus() - Method in class org.intermine.bio.util.OrganismData
-
Get the genus of this organism.
- getGlobalBag(String) - Method in class org.intermine.api.bag.BagManager
-
Fetch a global bag by name.
- getGlobalBags() - Method in class org.intermine.api.bag.BagManager
-
Fetch globally available bags - superuser public bags that are available to everyone.
- getGlobalBagsContainingId(Integer) - Method in class org.intermine.api.bag.BagManager
-
Fetch global bags that contain the given id.
- getGlobalBagsWithTags(List<String>) - Method in class org.intermine.api.bag.BagManager
-
Fetch globally available bags - superuser public bags that are available to everyone
with a particular tag assigned to them
- getGlobalSearchRepositories() - Static method in class org.intermine.api.search.SearchRepository
-
Get the search repositories registered as global repositories.
- getGlobalSearchRepository(Profile) - Static method in class org.intermine.api.search.SearchRepository
-
Get the search repository registered as global repositories for the user specified in input.
- getGlobalSearchRepository(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Get the SearchRepository for global (public) objects.
- getGlobalTemplate(String) - Method in class org.intermine.api.template.TemplateManager
-
Fetch a global template by name.
- getGlobalTemplates() - Method in class org.intermine.api.template.TemplateManager
-
Return a map from template name to template query containing superuser templates that are
tagged as public.
- getGlobalTemplates(boolean) - Method in class org.intermine.api.template.TemplateManager
-
Return a map from template name to template query containing superuser templates that are
tagged as public.
- getGOEvidence(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getGoIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a GO id resolver
- getGoIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a GO id resolver
- getGOTerms() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getGraphType() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
Get the type of this graph, e.g.
- getGroupBy() - Method in class org.intermine.objectstore.query.Query
-
Gets the GROUP BY clause of this Query
- getGroupBy() - Method in class org.intermine.sql.query.Query
-
Gets the Set of fields in the GROUP BY clause of this query.
- getGroupedConstraintLogic() - Method in class org.intermine.pathquery.PathQuery
-
Returns a List of logic Strings according to the different outer join sections of the query.
- getHasAvailableBags() - Method in class org.intermine.web.logic.query.MetadataNode
-
Returns true if there are any available bags for the type of this path.
- getHasClassKeys() - Method in class org.intermine.web.logic.query.MetadataNode
-
Returns true if the type of this path has class keys configured.
- getHasDisplayer() - Method in class org.intermine.web.logic.results.InlineTableResultElement
-
- getHasHeaderInlineLists() - Method in class org.intermine.web.logic.results.ReportObject
-
Used from JSP
- getHasMoreThanOneType() - Method in class org.intermine.web.logic.results.InlineResultsTable
-
- getHasNormalInlineLists() - Method in class org.intermine.web.logic.results.ReportObject
-
Used from JSP
- getHasPossibleLoops() - Method in class org.intermine.web.logic.query.MetadataNode
-
Returns true if this path in the query has possible loop constraints that are not already in
the query.
- getHasResults() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
- getHasResults() - Method in class org.intermine.web.logic.widget.GraphWidget
- getHasResults() - Method in class org.intermine.web.logic.widget.HTMLWidget
-
- getHasResults() - Method in class org.intermine.web.logic.widget.TableWidget
- getHasResults() - Method in class org.intermine.web.logic.widget.Widget
-
- getHasSubclasses() - Method in class org.intermine.web.logic.query.MetadataNode
-
Returns true if the original type has subclasses in the model.
- getHaving() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- getHaving() - Method in class org.intermine.sql.query.Query
-
Gets the set of constraints forming the HAVING clause of this query.
- getHavingBuffer() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- getHeadAttributes() - Method in class org.intermine.api.template.ApiTemplate
-
- getHeadAttributes() - Method in class org.intermine.pathquery.PathQuery
-
- getHeadAttributes() - Method in class org.intermine.template.TemplateQuery
-
- getHeader(String) - Method in interface org.intermine.webservice.client.core.Request
-
Returns the header value.
- getHeader(String) - Method in class org.intermine.webservice.client.core.RequestImpl
-
Returns the header value.
- getHeader() - Static method in class org.intermine.xml.full.FullRenderer
-
Return the Full XML file header
- getHeaderAttributes() - Method in class org.intermine.webservice.server.clob.SequenceService
-
Why is the results key "features", pray?
- getHeaderAttributes() - Method in class org.intermine.webservice.server.core.JSONService
-
Get the header attributes to apply to the formatter.
- getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListMakerService
-
- getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationDetailsService
-
- getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListTagService
-
- getHeaderAttributes() - Method in class org.intermine.webservice.server.lists.ListUploadService
-
Gets the header attributes on the output object.
- getHeaderAttributes() - Method in class org.intermine.webservice.server.output.Output
-
- getHeaderAttributes() - Method in class org.intermine.webservice.server.path.PossibleValuesService
-
- getHeaderAttributes() - Method in class org.intermine.webservice.server.search.QuickSearch
-
- getHeaderAttributes() - Method in class org.intermine.webservice.server.user.NewUserService
-
- getHeaderAttributes() - Method in class org.intermine.webservice.server.VersionService
-
- getHeaderAttributes() - Method in class org.intermine.webservice.server.widget.AvailableWidgetsService
-
- getHeaderAttributes() - Method in class org.intermine.webservice.server.widget.WidgetService
-
- getHeaderConfigLink() - Method in class org.intermine.web.logic.config.Type
-
- getHeaderConfigTitle() - Method in class org.intermine.web.logic.config.Type
-
- getHeaderInlineLists() - Method in class org.intermine.web.logic.results.ReportObject
-
- getHeaderLink() - Method in class org.intermine.web.logic.results.ReportObject
-
- getHeaders() - Method in interface org.intermine.webservice.client.core.Request
-
Returns request headers.
- getHeaders() - Method in class org.intermine.webservice.client.core.RequestImpl
-
Returns request headers.
- getHeadResources(String, Map<String, String>) - Static method in class org.intermine.web.logic.WebUtil
-
Returns the resources for a particular section of the head element.
- getHelper(Class<?>) - Static method in class org.intermine.api.query.MainHelper.RangeConfig
-
- getHelpMessage() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Return a help message to display alongside the constraint, this will examine the constraint
type and generate and appropriate message, e.g. list the key fields for LOOKUP constraints
and explain the use of wildcards.
- getHelpMessage(DisplayConstraint) - Static method in class org.intermine.web.logic.query.DisplayConstraintHelpMessages
-
Generate a context sensitive help message for a constraint.
- getHelpPage(HttpServletRequest) - Static method in class org.intermine.web.logic.WebUtil
-
Look at the current webapp page and subtab and return the help page and
tab.
- getHgncIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a HGNC human gene id resolver
- getHgncIdResolver(boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a HGNC human gene resolver
- getHide() - Method in class org.intermine.web.logic.config.FieldConfig
-
Return the value of the hide flag.
- getHighlight() - Method in class org.intermine.web.struts.WidgetForm
-
- getHighlightedLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
-
Returns html formatted link in which are highlighted parameters that
are to be replaced. * @see #getLink(String, TemplateQuery)
- getHintCount(String) - Method in class org.intermine.web.logic.results.WebState
-
Get the number of times a particular hint has been shown.
- getHintForPage(String, WebState) - Method in class org.intermine.web.logic.help.HintManager
-
Fetch a hint for the given page or return null if there are no hints or all hints have been
displayed the maximum number of times.
- getHistory() - Method in class org.intermine.api.profile.Profile
-
Get the session query history.
- getHits() - Method in class org.intermine.api.lucene.ResultsWithFacets
-
- getHtmlHeadTitle() - Method in class org.intermine.web.logic.results.ReportObject
-
Fetch a header string to use as the page title.
- getHtmlLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
-
Generates TemplateResultService web service link.
- getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.BadRequestException
-
- getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.InternalErrorException
-
- getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.NotImplementedException
-
- getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.ResourceNotFoundException
-
- getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.ServiceException
-
- getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.ServiceForbiddenException
-
- getHttpErrorCode() - Method in exception org.intermine.webservice.client.exceptions.ServiceUnavailableException
-
- getHttpErrorCode() - Method in exception org.intermine.webservice.server.exceptions.ServiceException
-
- getHumanIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a Human gene id resolver
- getHumanIdResolver(boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a Human gene resolver
- getIcon(int) - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
-
- getIcon(int) - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
-
- getIconImage() - Method in class org.intermine.web.logic.aspects.Aspect
-
Get the icon Image.
- getID() - Method in class org.intermine.api.mines.LocalMine
-
- getId() - Method in interface org.intermine.api.results.ResultCell
-
- getId() - Method in class org.intermine.api.results.ResultElement
-
Get the Id.
- getId() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the first value of the Id field from the attributes of this record.
- getId() - Method in class org.intermine.bio.ontology.OboTerm
-
Get the id of this term.
- getId() - Method in class org.intermine.bio.ontology.OboTypeDefinition
-
- getId() - Method in interface org.intermine.model.InterMineObject
-
Getter for the ID field - ensures that every object in the database has an ID.
- getId() - Method in class org.intermine.objectstore.proxy.ProxyReference
-
Gets the ID value
- getId() - Method in class org.intermine.web.logic.config.InlineListObject
-
- getId() - Method in class org.intermine.web.logic.config.TableExportConfig
-
Return the id of this TableExportConfig.
- getId() - Method in class org.intermine.web.logic.results.DisplayReference
-
Get the id of the object
- getId() - Method in class org.intermine.web.logic.results.ReportObject
-
Get the id of this object
- getId() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- getId() - Method in class org.intermine.web.search.KeywordSearchResult
-
intermine ID
- getId() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
-
- getId() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
-
Gets element id.
- getId() - Method in class org.intermine.webservice.client.results.Item
-
Get the internal database id of the object.
- getId() - Method in class org.intermine.webservice.server.core.TableCell
-
- getIdentifier() - Method in class org.intermine.api.beans.ObjectDetails
-
- getIdentifier() - Method in class org.intermine.api.mines.ObjectRequest
-
- getIdentifier(Sequence) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
For the given BioJava Sequence object, return an identifier to be used when creating
the corresponding BioEntity.
- getIdentifier(Sequence) - Method in class org.intermine.bio.dataconversion.FlyBaseCDSFastaLoaderTask
-
For the given BioJava Sequence object, return an identifier to be used when creating
the corresponding BioEntity.
- getIdentifier(Sequence) - Method in class org.intermine.bio.dataconversion.FlyBaseUTRFastaLoaderTask
-
For the given BioJava Sequence object, return an identifier to be used when creating
the corresponding BioEntity.
- getIdentifier(Sequence) - Method in class org.intermine.bio.dataconversion.NCBIFastaLoaderTask
-
For the given BioJava Sequence object, return an identifier to be used when creating
the corresponding BioEntity.
- getIdentifier() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
-
Used from JSP
- getIdentifier() - Method in class org.intermine.xml.full.Item
-
Get the identifier of this item.
- getIdentifierFields() - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
-
which fields in gene object we are setting, eg. primaryIdentifier or secondaryIdentifier
- getIdentifierMethod(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
-
- getIdentifierMethod(String, String) - Method in class org.intermine.bio.dataconversion.UniprotConfig
-
- getIdentifierName() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
-
- getIdentifierSource() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
-
Where we should get the identifier will either be an Xref database, e.g.
- getIdentifierValue(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
-
- getIdentifierValue(String, String) - Method in class org.intermine.bio.dataconversion.UniprotConfig
-
- getIdentity() - Method in class org.intermine.webservice.server.JWTVerifier.Verification
-
- getIdField() - Method in class org.intermine.sql.writebatch.TableBatch
-
Returns the idField.
- getIdMap() - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
-
Returns the IdMap used.
- getIdResolver() - Method in class org.intermine.bio.dataconversion.DoNothingIdResolverFactory
-
- getIdResolver(String) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
Return an IdResolver by taxon id, if not already built then create it.
- getIdResolver(Set<String>) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
Return an IdResolver by a list of taxon id, if not already built then create it.
- getIdResolver(String, boolean) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
Return an IdResolver by taxon id, if not already built then create it.
- getIdResolver(Set<String>, boolean) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
Return an IdResolver by a list of taxon ids, if not already built then create it.
- getIdResolver() - Method in class org.intermine.bio.dataconversion.IdResolverFactory
-
Return an IdResolver, if not already built then create it.
- getIdResolver(boolean) - Method in class org.intermine.bio.dataconversion.IdResolverFactory
-
Return an IdResolver, if not already built then create it.
- getIdResolver() - Method in class org.intermine.bio.dataconversion.MockIdResolverFactory
-
Create a MockIdResolver
- getIdResolver() - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory
-
Return an IdResolver, if not already built then create it.
- getIdResolver(boolean) - Method in class org.intermine.bio.dataconversion.OntologyIdResolverFactory
-
Return an IdResolver, if not already built then create it.
- getIdResolverByOrganism(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a Entrez Gene Id Resolver by given taxonId
- getIdResolverByOrganism(Set<String>) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a Entrez Gene Id Resolver by given taxonId set
- getIdResolverByTaxonId(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a Entrez Gene Id Resolver by given taxonId
- getIdResolverByTaxonId(Set<String>, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a Entrez Gene Id Resolver by given taxonId set
- getIdResolverForMOD() - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
- getIds() - Method in interface org.intermine.api.idresolution.JobInput
-
- getIds() - Method in class org.intermine.objectstore.query.QueryClassBag
-
Returns the Set of object IDs present in the bag that correspond to the type specified.
- getIds(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
-
Get the ids for a constraint.
- getIds() - Method in class org.intermine.pathquery.PathConstraintIds
-
Returns the id collection that the constraint is constraining to.
- getIds() - Method in class org.intermine.web.logic.bag.WebJobInput
-
- getIdsContained(Collection<Integer>) - Method in class org.intermine.api.profile.InterMineBag
-
Returns a List which contains the ids given in input and contained
in this bag as Integer IDs.
- getIdsToDelete() - Method in class org.intermine.sql.writebatch.TableBatch
-
Returns the delete set.
- getIdsToInsert() - Method in class org.intermine.sql.writebatch.TableBatch
-
Returns the insert map.
- getIdsToRemove(InterMineBag) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Get the IDs to remove.
- getIgnoredTaxonIds() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
used for testing
- getImage() - Method in class org.intermine.web.logic.config.HeaderConfigLink
-
- getImplementations() - Method in class org.intermine.xml.full.Item
-
Get the interfaces implemented by this item.
- getImplementClassDescriptors(String) - Method in class org.intermine.xml.full.Item
-
Returns the ClassDescriptors for the given implementations.
- getImplements(Object, Model) - Static method in class org.intermine.xml.full.ItemFactory
-
Get all interfaces that an object implements.
- getIncludeHeaders() - Method in class org.intermine.web.struts.TableExportForm
-
Return the current value of the includeHeaders flag.
- getIndelResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Return a result set containing pairs of chromosome_structure_variation (deletions) and
transposable_element_insertion_site (insertions).
- getIndentation() - Method in class org.intermine.pathquery.Node
-
Gets the value of indentation
- getIndentation() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
-
Returns the number of elements in the path, where a simple class is zero.
- getIndentation() - Method in class org.intermine.web.logic.TreeNode
-
Get the indentation
- getIndex() - Method in class org.intermine.api.results.Column
-
Gets the value of index
- getIndexSearch() - Method in class org.intermine.web.autocompletion.LuceneSearchEngine
-
returns the indexSearcher so we can use IndexSearcher.doc(int) to get a
doc
- getIndexWriter(boolean, String) - Method in class org.intermine.web.autocompletion.LuceneIndex
-
returns the index writer
- getIndirectAlias() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- getIndirectionTableName(CollectionDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
-
Creates an indirection table name for a many-to-many collection descriptor
- getIndirectionTableNames(ClassDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
-
Given a ClassDescriptor find names of all related indirection tables.
- getInfo() - Method in class org.intermine.api.results.WebResults
-
Return the ResultsInfo object from the underlying Results object.
- getInfo() - Method in interface org.intermine.api.results.WebTable
-
Gets the underlying results object info
- getInfo() - Method in interface org.intermine.objectstore.proxy.LazyCollection
-
Returns Returns the current best estimate of the characteristics of the LazyCollection
- getInfo() - Method in class org.intermine.objectstore.proxy.ProxyCollection
-
Returns Returns the current best estimate of the characteristics of the LazyCollection
- getInfo() - Method in class org.intermine.objectstore.query.Results
-
Gets the best current estimate of the characteristics of the query.
- getInfo() - Method in class org.intermine.objectstore.query.ResultsBatches
-
Gets the best current estimate of the characteristics of the query.
- getInfoCache() - Method in class org.intermine.api.query.WebResultsExecutor
-
Returns the entire infoCache, which is an unmodifiable Map from PathQuery (by identity) to
ResultsInfo.
- getInitialExportPaths(PagedTable) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
-
The initial export path list is just the paths from the columns of the PagedTable.
- getInitialExportPaths(PagedTable) - Method in interface org.intermine.web.logic.export.http.TableHttpExporter
-
Return a list of the Paths to show the user as initial export columns or header contents.
- getInlineListConfig() - Method in class org.intermine.web.logic.config.Type
-
- getInput() - Method in class org.intermine.api.idresolution.ResolutionJob
-
- getInput() - Method in class org.intermine.webservice.server.lists.AbstractListService
-
- getInput() - Method in interface org.intermine.webservice.server.lists.ListMaker
-
- getInput() - Method in class org.intermine.webservice.server.lists.ListOperationService
-
- getInput() - Method in class org.intermine.webservice.server.lists.ListsRequestParser
-
Returns parameters of web service as a parameter object.
- getInput() - Method in class org.intermine.webservice.server.lists.ListSubtractionService
-
- getInput() - Method in class org.intermine.webservice.server.lists.ListUploadService
-
Parse the parameters for this request.
- getInput() - Method in class org.intermine.webservice.server.query.result.QueryResultRequestParser
-
Returns parsed parameters in parameter object - so this
values can be easily get from this object.
- getInput() - Method in class org.intermine.webservice.server.template.result.TemplateResultRequestParser
-
Returns parsed parameters in parameter object - so this
values can be easily obtained from this object.
- getInput(HttpServletRequest) - Method in class org.intermine.webservice.server.widget.WidgetsRequestParser
-
Returns parameters of web service as a parameter object.
- getInputIdent() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
-
- getInputIdentifiersForIssue(String) - Method in class org.intermine.api.bag.BagQueryResult
-
- getInsertionLocationsResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Return a result set containing pairs of insertion feature_ids (eg. for "FBti0027974" =>
"FBti0023081") and the fmin and fmax of the first insertion in the pair (ie. the progenitor).
- getInstance(ProfileManager) - Static method in class org.intermine.api.bag.SharedBagManager
-
Return the singleton SharedBagManager instance
- getInstance() - Static method in class org.intermine.api.idresolution.IDResolver
-
- getInstance(InterMineAPI, Properties) - Static method in class org.intermine.api.mines.FriendlyMineManager
-
Get an instance of FriendlyMineManager.
- getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.KeySearchTracker
-
Return an instance of the KeySearchTracker
- getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.ListTracker
-
Return an instance of the ListTracker
- getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.LoginTracker
-
Return an instance of the LoginTracker
- getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.QueryTracker
-
Return an instance of the QueryTracker
- getInstance(Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.TemplateTracker
-
Return an instance of the TemplateTracker
- getInstance(String, Properties) - Static method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
-
Creates a new instance of this class, given the properties defining it.
- getInstance(String, Properties, Class<? extends IntegrationWriterDataTrackingImpl>, Class<? extends DataTracker>) - Static method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
-
Creates a new IntegrationWriter instance of the specified class and with a specified
DataTracker class plus properties.
- getInstance(String, Properties) - Static method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
-
Gets an ObjectStoreFastCollectionsForTranslatorImpl instance for the given properties
- getInstance(String, Properties) - Static method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
-
Gets an ObjectStoreFastCollectionsImpl instance for the given properties
- getInstance(String, Properties) - Static method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Gets a ObjectStoreInterMineImpl instance for the given underlying properties
- getInstance(String, Properties) - Static method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
-
Gets an ObjectStore for the given underlying properties.
- getInstance() - Static method in class org.intermine.pathquery.PathLengthComparator
-
- getInstance(Database) - Static method in class org.intermine.sql.precompute.OptimiserCache
-
Returns an OptimiserCache object relevant to the database given.
- getInstance(Connection) - Static method in class org.intermine.sql.precompute.PrecomputedTableManager
-
Gets a PrecomputedTableManager instance for the given underlying Connection.
- getInstance(Database) - Static method in class org.intermine.sql.precompute.PrecomputedTableManager
-
Gets a PrecomputedTableManager instance for the given underlying database.
- getInstance(String, Connection) - Static method in class org.intermine.sql.query.ExplainResult
-
Constructs an instance of ExplainResult for a given query String and
database Connection.
- getInstance(Query, Connection) - Static method in class org.intermine.sql.query.ExplainResult
-
Constructs an instance of ExplainResult for a given Query and
database Connection.
- getInstance(PreparedStatement) - Static method in class org.intermine.sql.query.ExplainResult
-
Constructs an instance of ExplainResult given a PreparedStatement
object.
- getInstance() - Static method in class org.intermine.util.AlwaysSet
-
Returns a new AlwaysSet with the correct type parameters.
- getInstance() - Static method in class org.intermine.util.IdentityMap
-
Obtain an instance of this class
- getInstance() - Static method in class org.intermine.util.ShutdownHook
-
Get the instance of this ShutdownHook.
- getInstance(WebConfig, InterMineAPI) - Static method in class org.intermine.web.displayer.DisplayerManager
-
Fetch the DisplayerManager, a single instance is held.
- getInstance(Properties) - Static method in class org.intermine.web.logic.help.HintManager
-
Return an instance of a HintManager.
- getInstance() - Static method in class org.intermine.webservice.server.user.DeletionTokens
-
- getInt(String) - Method in class org.intermine.webservice.client.results.Item
-
Get a property known to be an integer.
- getIntegrationWriter() - Method in class org.intermine.dataloader.DataLoader
-
Return the IntegrationWriter that was passed to the constructor.
- getIntegrationWriter(String) - Static method in class org.intermine.dataloader.IntegrationWriterFactory
-
Return an IntegrationWriter configured using properties file
- getIntegrationWriter() - Method in class org.intermine.task.DirectDataLoaderTask
-
Return the IntegrationWriter for this task.
- getInteractionResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Return a result set containing the interaction genes pairs, the title of the publication
that reported the interaction and its pubmed id.
- getInterMineAPI() - Static method in class org.intermine.web.context.InterMineContext
-
- getInterMineAPI(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Get the InterMineAPI which provides access to core features of an InterMine application.
- getInterMineAPI(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Get the InterMineAPI which provides the core features of an InterMine application.
- getInterMineAPI(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Get the InterMineAPI which provides access to core features of an InterMine application.
- getInterMineResults() - Method in class org.intermine.api.results.WebResults
-
Return the underlying results object.
- getIntParameter(String) - Method in class org.intermine.webservice.server.WebService
-
Get the value of a parameter that should be interpreted as an integer.
- getIntParameter(String, Integer) - Method in class org.intermine.webservice.server.WebService
-
Get the value of a parameter that should be interpreted as an integer.
- getIntResponse(Request) - Method in class org.intermine.webservice.client.core.Service
-
Performs the request and returns the result as an integer.
- getIntroText() - Method in class org.intermine.web.logic.aspects.Aspect
-
Get the introduction text.
- getIntSessionProperty(HttpSession, String, int) - Static method in class org.intermine.web.logic.WebUtil
-
Lookup an Integer property from the SessionContext and return it.
- getInvalidBags() - Method in class org.intermine.api.profile.BagSet
-
- getInvalidBags() - Method in class org.intermine.api.profile.Profile
-
- getInvalidQuery() - Method in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
-
- getInvalidQuery() - Method in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
-
- getInvalidQuery() - Method in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
-
- getInvite() - Method in class org.intermine.web.struts.InvitationForm
-
- getInviteData(ProfileManager, Profile) - Static method in class org.intermine.api.bag.SharingInvite
-
- getInvitee() - Method in class org.intermine.api.bag.SharingInvite
-
- getInvitee() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
-
- getInviterId() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
-
- getInvites(InterMineAPI, Profile) - Static method in class org.intermine.api.bag.SharingInvite
-
Get the invitations this profile has made.
- getInvites(ProfileManager, BagManager, Profile) - Static method in class org.intermine.api.bag.SharingInvite
-
Get the invitations this profile has made.
- getInwardIndirectionColumnName(CollectionDescriptor, int) - Static method in class org.intermine.sql.DatabaseUtil
-
Creates a column name for the "inward" key of a many-to-many collection descriptor.
- getIqlQuery() - Method in class org.intermine.objectstore.query.Query
-
Returns an IqlQuery object representing this query, that may have been cached.
- getIsDottedPath() - Method in class org.intermine.web.logic.config.FieldConfig
-
- getIsKeyField() - Method in class org.intermine.web.logic.results.InlineTableResultElement
-
- getIsNull() - Method in class org.intermine.web.logic.query.MetadataNode
-
- getIsoforms() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getIsoformSynonyms() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
if an isoform has two ID tags, then the first one is used and the second one is added
as a synonym
- getIsRelative() - Method in class org.intermine.web.logic.WebUtil.HeadResource
-
- getIssueIds() - Method in class org.intermine.api.bag.BagQueryResult
-
Get ids of all InterMineObjects returned that were issues for this
bag query lookup.
- getIssueIds(String) - Method in class org.intermine.api.bag.BagQueryResult
-
Get ids of all InterMineObjects returned that were registered as
issues of this particular type for this bag query lookup.
- getIssuer() - Method in class org.intermine.webservice.server.JWTVerifier.Verification
-
- getIssueResults(String) - Method in class org.intermine.api.bag.BagQueryResult
-
- getIssues() - Method in class org.intermine.api.bag.BagQueryResult
-
Get any results that require some user input before adding to the bag.
- getItem() - Method in class org.intermine.api.search.SearchResult
-
Get the web searchable item that was found.
- getItemElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
-
- getItemElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
-
- getItemRgb() - Method in class org.intermine.bio.io.bed.BEDRecord
-
- getItemRgb() - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- getItems() - Method in class org.intermine.api.lucene.KeywordSearchFacet
-
list of all values and counts
- getItems() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Return all items set and created in handler in this run - excludes sequence and
ComputationalAnalysis items.
- getItems() - Method in class org.intermine.dataconversion.MockItemWriter
-
Get the items that have been stored
This method is not part of ItemWriter, and for testing convenience returns XML Items
- getItems() - Method in class org.intermine.web.logic.results.InlineList
-
- getItems() - Method in class org.intermine.web.logic.results.InlineResultsTableRow
-
- getItems() - Method in class org.intermine.xml.full.FullHandler
-
Return the Items that have been read with this handler.
- getItemWriter() - Method in class org.intermine.bio.dataconversion.ChadoProcessor
-
Return an ItemWriter used to handle the resultant Items
- getItemWriter() - Method in class org.intermine.dataconversion.DataConverter
-
Return the ItemWriter that was passed to the constructor.
- getIterator() - Method in class org.intermine.webservice.client.results.JSONResult
-
- getIterator() - Method in class org.intermine.webservice.client.results.TabTableResult
-
Get a memory efficient iterator over the result rows as lists
- getIterator() - Method in class org.intermine.webservice.client.results.XMLTableResult
- getJavaClass() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Get the Java class name of the controller for this displayer.
- getJobById(UUID) - Method in class org.intermine.api.idresolution.IDResolver
-
- getJobById(String) - Method in class org.intermine.api.idresolution.IDResolver
-
- getJobs() - Method in class org.intermine.api.idresolution.IDResolver
-
- getJoinPath() - Method in class org.intermine.webservice.server.core.SubTable
-
- getJoinType() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
- getJson() - Method in class org.intermine.pathquery.PathQuery
-
toJson synonym for JSPs.
- getJSONResponse(Request) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Performs the request and returns a JSONResult containing the data.
- getJSONResults(PathQuery, Page) - Method in class org.intermine.webservice.client.services.QueryService
-
- getJSONResults(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
-
Fetch some results as a list of JSON Objects.
- getJSONResults(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
-
Returns a subset of the results for the given template template with the given parameters,
as JSON objects (see @link {http://www.intermine.org/wiki/JSONObjectFormat}).
- getJSONResults(TemplateQuery, Page) - Method in class org.intermine.webservice.client.services.TemplateService
-
- getJspName() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Get the name of the JSP associated with this displayer.
- getJspPage() - Method in class org.intermine.web.displayer.ReportDisplayer
-
The JSP page that will be called with the request to render output.
- getKey() - Method in interface org.intermine.util.ReferenceMap.ReferenceWithKey
-
Returns the key in the entry.
- getKey() - Method in class org.intermine.web.logic.WebUtil.HeadResource
-
- getKey() - Method in class org.intermine.webservice.server.core.Pair
-
- getKeyFieldNames(Map<String, List<FieldDescriptor>>, String) - Static method in class org.intermine.api.config.ClassKeyHelper
-
Return names of the key fields for a given class.
- getKeyFieldNames() - Method in class org.intermine.api.profile.InterMineBag
-
Return a list containing the keyFieldNames for the bag
- getKeyFields(Map<String, List<FieldDescriptor>>, String) - Static method in class org.intermine.api.config.ClassKeyHelper
-
Return the key fields of a given class.
- getKeyFields() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Return the key fields for this path as a formatted string, for use in LOOKUP help message.
- getKeyFields() - Method in class org.intermine.web.search.KeywordSearchResult
-
key field expressions
- getKeyFieldValue(FastPathObject, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.config.ClassKeyHelper
-
Get a key field value for the given object.
- getKeyFieldValues(FastPathObject, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.config.ClassKeyHelper
-
Get a list of key field values for the given object.
- getKeyProperties(Source) - Static method in class org.intermine.dataloader.DataLoaderHelper
-
Return the Properties that enumerate the keys for this Source
- getKeyStore() - Static method in class org.intermine.web.context.InterMineContext
-
- getKeywords() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getKeywordSearches(Connection) - Method in class org.intermine.api.tracker.KeySearchTracker
-
Return the number of search for each keyword
- getKeywordSearches() - Method in class org.intermine.api.tracker.TrackerDelegate
-
Return the number of search for each keyword
- getLabel() - Method in class org.intermine.web.logic.config.FieldConfig
-
The human readable label for this field.
- getLabel() - Method in class org.intermine.web.logic.config.Type
-
Get the label property's value.
- getLabel() - Method in class org.intermine.web.logic.query.DisplayConstraint.DisplayConstraintOption
-
Get the value to be displayed in the dropdown for this operation.
- getLabel() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- getLabel() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
label for the results table.
- getLabel() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
-
Get the label for this trail element.
- getLabels() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
-
Get additional display labels for attribute values in the enrichment analysis, these may be
names where the values analysed were identifiers.
- getLabels() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
-
- getLabels() - Method in class org.intermine.web.logic.widget.EnrichmentResults
-
Get additional display labels for attribute values in the enrichment analysis, these may be
names where the values analysed were identifiers.
- getLabels(GraphWidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetProcessorImpl
-
Get the labels for Graph widgets.
- getLabs(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the lab name.
- getLargeImage() - Method in class org.intermine.web.logic.aspects.Aspect
-
Webapp relative path to large image.
- getLastClassDescriptor() - Method in class org.intermine.pathquery.Path
-
Returns the last ClassDescriptor in the path.
- getLastClassName() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
-
Fetch the unqualified class name of the final class on this path, if the path represents an
attribute this will be the parent class of that attribute.
- getLastElement() - Method in class org.intermine.pathquery.Path
-
Return the last string element of this path, throw an exception of there is only one element,
i.e. for 'Company.departments.manager' return 'manager'.
- getLayout() - Method in class org.intermine.web.logic.template.TemplateResultInput
-
- getLayout() - Method in class org.intermine.webservice.server.query.result.QueryResultInput
-
- getLdr() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- getLeft() - Method in class org.intermine.objectstore.query.OverlapConstraint
-
Returns the left OverlapRange.
- getLeft() - Method in class org.intermine.sql.query.Constraint
-
Returns the left argument of the constraint.
- getLeft() - Method in class org.intermine.sql.query.InListConstraint
-
Returns the left AbstractValue.
- getLeft() - Method in class org.intermine.sql.writebatch.Row
-
Returns left.
- getLeftArgument(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
-
Get the left argument of the given constraint, will return null
if passed a ConstraintSet or a MultipleInBagConstraint.
- getLeftColName() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
-
Returns the left column name.
- getLeftField() - Method in class org.intermine.api.query.range.ConstraintOptions
-
Defaults to "start".
- getLeftOp() - Method in class org.intermine.api.query.range.ConstraintOptions
-
- getLength() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getLength() - Method in class org.intermine.web.logic.results.InlineList
-
- getLengthWithoutInit() - Method in class org.intermine.objectstore.query.ClobAccess
-
Returns the (possibly uninitialised) length internal parameter in this object, for use by
subclass constructors.
- getLevel() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
-
- getLibraryCVTermResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return the interesting rows from the librarycvterm table.
- getLibraryFeatureResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return the interesting rows from the libraryprop table.
- getLimit() - Method in class org.intermine.objectstore.query.Query
-
Returns the LIMIT parameter for this query.
- getLimit() - Method in class org.intermine.sql.precompute.LimitOffsetQuery
-
Getter for limit.
- getLimit() - Method in class org.intermine.sql.query.Query
-
Gets the LIMIT number for this query.
- getLimit() - Method in class org.intermine.webservice.server.WebServiceInput
-
Returns maximum number of results the user will accept.
- getLineBreak() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
-
- getLineBreak() - Method in class org.intermine.webservice.server.WebService
-
- getLineLength() - Method in class org.intermine.web.logic.config.InlineListConfig
-
- getLineLength() - Method in class org.intermine.web.logic.results.InlineList
-
- getLink() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
the link is the class that generates the url for each result.
- getLink() - Method in class org.intermine.web.struts.WidgetForm
-
- getLink() - Method in class org.intermine.web.tags.disclosure.DisclosureHeadTag
-
- getLink() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
-
Returns link switching between displayed and hidden state.
- getLink(String, String, String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
-
Generates QueryResultService web service link.
- getLinkPath(String, String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
-
Get the link path for a query.
- getLinkPath(TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
-
Returns the path section of the link for this template.
- getLinkPath(TemplateQuery, String) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
-
Returns the path section of the link for this template.
- getLinkPath(TemplateQuery, String, boolean) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
-
Returns the path section of the link for this template.
- getLinkRedirect() - Method in class org.intermine.api.results.ResultElement
-
- getLinkRedirect() - Method in class org.intermine.web.search.KeywordSearchResult
-
URL set in web.properties.
- getLinkRedirector() - Method in interface org.intermine.api.API
-
- getLinkRedirector() - Method in class org.intermine.api.InterMineAPI
-
- getLinks(MultiKey) - Method in class org.intermine.api.mines.FriendlyMineManager
-
- getLinks(Mine, Mine, ObjectRequest) - Method in interface org.intermine.web.displayer.InterMineLinkGenerator
-
Query other intermines for this object
- getLinks(FriendlyMineManager, String, String, String) - Method in class org.intermine.web.util.InterMineLinkGenerator
-
Query other intermines for this object
- getList(String, String) - Method in class org.intermine.web.autocompletion.AutoCompleter
-
returns a string array with the search results of the query in the field
- getList(String) - Method in class org.intermine.webservice.client.services.ListService
-
Returns an object representing a list on the server.
- getList(Profile, String) - Method in class org.intermine.webservice.server.query.QueryListAppendService
-
Get a list from a profile, throwing a service forbidden exception if the list is not
accessible.
- getListCreationTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices
-
- getListCreationTrend() - Method in class org.intermine.dwr.TrackAjaxServices
-
- getListExecutionTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices
-
- getListExecutionTrend() - Method in class org.intermine.dwr.TrackAjaxServices
-
- getListIterator() - Method in class org.intermine.webservice.client.results.RowResultSet
-
Get a memory efficient iterator over the result rows as lists
- getListLeft() - Method in class org.intermine.web.struts.ModifyBagForm
-
- getListManager() - Method in class org.intermine.webservice.server.WebService
-
- getListMap() - Method in class org.intermine.webservice.client.services.ListService
-
Returns a map from list-name to list.
- getListMap() - Method in class org.intermine.webservice.server.core.ListManager
-
Returns the lists available to the current user in a Map.
- getListName() - Method in class org.intermine.webservice.server.lists.ListInput
-
- getListOfTypes() - Method in class org.intermine.web.logic.results.InlineResultsTable
-
- getListOperations(Connection) - Method in class org.intermine.api.tracker.ListTracker
-
Return the operations done for each list (execution or creation)
- getListOperations() - Method in class org.intermine.api.tracker.TrackerDelegate
-
Return the operations done for each list (execution or creation)
- getListPath() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- getListRight() - Method in class org.intermine.web.struts.ModifyBagForm
-
- getLists() - Method in class org.intermine.webservice.server.core.ListManager
-
Returns the lists available to the current user.
- getLists() - Method in class org.intermine.webservice.server.lists.AsymmetricOperationInput
-
- getLists() - Method in class org.intermine.webservice.server.lists.AvailableListsService
-
Get the lists for this request.
- getLists() - Method in class org.intermine.webservice.server.lists.ListInput
-
- getLists() - Method in class org.intermine.webservice.server.lists.ListsService
-
Executes service specific logic.
- getListsButton() - Method in class org.intermine.web.struts.ModifyBagForm
-
- getListsContaining(Integer) - Method in class org.intermine.webservice.server.core.ListManager
-
Returns the current lists available to the current user which contain the
specified object.
- getListService() - Method in class org.intermine.webservice.client.core.ServiceFactory
-
Return a new ListService for getting getting list information from.
- getListsMatching(ListManager, String) - Method in class org.intermine.webservice.server.lists.AvailableListsService
-
Get the lists that match the current filter.
- getListsNames(Integer) - Method in class org.intermine.webservice.server.core.ListManager
-
Returns public current lists that contain object with specified id.
- getListsWithObject(String, String) - Method in class org.intermine.webservice.client.services.ListService
-
Returns all accessible InterMine lists containing the object corresponding
to the specified publicId.
- getListsWithObject(int) - Method in class org.intermine.webservice.client.services.ListService
-
Returns all accessible InterMine public lists containing the object
with the specified DB identifier.
- getListUploadTokeniser() - Static method in class org.intermine.api.query.LookupTokeniser
-
Return a tokeniser suitable for parsing tokens received from a list upload context.
- getLocalMine() - Method in class org.intermine.api.mines.FriendlyMineManager
-
- getLocatedGenesResultSet(Connection) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Return from chado the feature_ids of the genes with entries in the featureloc table.
- getLocation() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Return the location Item set by setLocation()
- getLocationFromHeader(String, SequenceFeature, Organism) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
-
Return a Location object create by parsing the useful information from a FlyBase fasta
header line.
- getLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Returns the log used by this objectstore.
- getLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Returns the log used by this objectstore.
- getLogarithmMap(String, TemplateManager) - Method in class org.intermine.api.tracker.TemplatesExecutionMap
-
Return a map containing the logarithm's sum of the templates executions launched by
the same users or during the same sessions.
- getLogarithmMap(String, String, TemplateManager) - Method in class org.intermine.api.tracker.TemplateTracker
-
Return a map containing the logarithm of accesses for each template.
- getLogBeforeExecute() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Gets the logBeforeExecute configuration option.
- getLogBeforeExecute() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Gets the logBeforeExecute configuration option.
- getLogEverything() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Gets the logEverything configuration option.
- getLogEverything() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Gets the logEverything configuration option.
- getLogExplains() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Gets the logExplains configuration option.
- getLogExplains() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Gets the logExplains configuration option.
- getLogicExpression() - Method in class org.intermine.pathquery.PathQuery
-
- getLoginTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices
-
- getLogo() - Method in class org.intermine.api.mines.LocalMine
-
- getLogo() - Method in interface org.intermine.api.mines.Mine
-
- getLogo() - Method in class org.intermine.api.mines.RemoteMine
-
- getLongDisplayers() - Method in class org.intermine.web.logic.config.Type
-
Get the List of long Displayers
- getLookupOp() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Return the LOOKUP constraint op.
- getLookupOs() - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
-
Returns the objectstore that contains the equivalent objects.
- getLookupTokeniser() - Static method in class org.intermine.api.query.LookupTokeniser
-
Return a tokeniser suitable for parsing tokens received from a lookup constraint context.
- getLoopPath() - Method in class org.intermine.pathquery.PathConstraintLoop
-
Returns the path that the constraint is constraining to.
- getLoopQueryOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Gets the value of loopQueryOp
- getLoopQueryOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Returns the set of operators valid for loop constraints.
- getLoopQueryValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Gets the value of loopQueryValue
- getMailinglist() - Method in class org.intermine.web.struts.CreateAccountForm
-
- getMainIds() - Method in class org.intermine.bio.dataconversion.GeneInfoRecord
-
Return the entrez gene id, official symbol and default symbol (if different).
- getMainSetOp() - Method in class org.intermine.api.query.range.ConstraintOptions
-
- getMainSource(String, String) - Method in interface org.intermine.dataloader.IntegrationWriter
-
Converts a string describing the data source into a Source object suitable for passing to the
store method as the main source.
- getMainSource(String, String) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
-
Converts a string describing the data source into a Source object suitable for passing to the
store method as the main source.
- getMainTitles() - Method in class org.intermine.web.logic.config.Type
-
- getMap() - Method in class org.intermine.util.DynamicBean
-
Getter for the map, for testing purposes
- getMapIterator() - Method in class org.intermine.webservice.client.results.RowResultSet
-
Get a memory efficient iterator over the result rows as lists
- getMapper(TagMapper.Field) - Static method in class org.intermine.api.profile.TagMapper
-
Get a tag mapper.
- getMatchAndIssueIds() - Method in class org.intermine.api.bag.BagQueryResult
-
Get ids of all InterMineObjects returned that were matches or issues for this
bag query lookup.
- getMatcher() - Method in class org.intermine.webservice.server.lists.ListUploadService
-
Get the String Matcher for parsing the list of identifiers.
- getMatches() - Method in class org.intermine.api.bag.BagQueryResult
-
Get any exact matches found by the queries [id -> [input strings].
- getMatchIDs() - Method in class org.intermine.web.struts.BagUploadConfirmForm
-
Get the encoded match ids (hidden form field).
- getMatchLocResultSet(Connection, String) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
-
Return the interesting feature (EST, UST, RST, other?)
- getMatchLocResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return the interesting matches from the featureloc and feature tables.
- getMatchOnFirst() - Method in class org.intermine.api.bag.BagQueryConfig
-
If flag is true, bagqueryrunner queries for identifier until match is found, returning
only that first matching record.
- getMatchTypesResultSet(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
-
Return the match types, used to determine which additional query to run
This is a protected method so that it can be overridden for testing
- getMaterialisedCollection() - Method in class org.intermine.objectstore.proxy.ProxyCollection
-
Gets the collection if it is a real materialised collection.
- getMax(String) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
-
Return the maximum coordinate of the given location
- getMax() - Method in class org.intermine.objectstore.query.ResultsInfo
-
Returns the maximum possible number of rows in the results.
- getMax() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
maximum value to display.
- getMax() - Method in class org.intermine.web.struts.WidgetForm
-
- getMax() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary
-
- getMaxLimit() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Get the maximum LIMIT that can be used in an SQL query without throwing an
ObjectStoreLimitReachedException
- getMaxLimit() - Method in interface org.intermine.objectstore.ObjectStore
-
Get the maximum LIMIT that can be used in an SQL query without throwing an
ObjectStoreLimitReachedException
- getMaxLimit() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Get the maximum LIMIT that can be used in an SQL query without throwing an
ObjectStoreLimitReachedException
- getMaxLimit() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Get the maximum LIMIT that can be used in an SQL query without throwing an
ObjectStoreLimitReachedException
- getMaxOffset() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Get the maximum range start index a that can be accessed in a Results object without throwing
an ObjectStoreLimitReachedException
- getMaxOffset() - Method in interface org.intermine.objectstore.ObjectStore
-
Get the maximum range start index a that can be accessed in a Results object without throwing
an ObjectStoreLimitReachedException
- getMaxOffset() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Get the maximum range start index a that can be accessed in a Results object without throwing
an ObjectStoreLimitReachedException
- getMaxOffset() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Get the maximum range start index a that can be accessed in a Results object without throwing
an ObjectStoreLimitReachedException
- getMaxParam() - Method in class org.intermine.objectstore.query.WidthBucketFunction
-
- getMaxPValue() - Method in interface org.intermine.web.logic.widget.EnrichmentOptions
-
- getMaxPValue() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
-
- getMaxQueryParseTime() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
- getMaxQueryParseTime() - Method in class org.intermine.sql.precompute.QueryOptimiserContext
-
Get the maximum time in milliseconds that the optimiser should spend parsing a query from
SQL string to an org.intermine.sql.Query object.
- getMaxRetrievableIndex() - Method in class org.intermine.api.results.WebResults
-
Returns the ObjectStore's maximum allowable offset.
- getMaxRetrievableIndex() - Method in interface org.intermine.api.results.WebTable
-
Return the maximum retrievable index for this PagedTable.
- getMaxRetrievableIndex() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Return the maximum retrievable index for this PagedTable.
- getMaxSize() - Method in class org.intermine.objectstore.query.ResultsBatches
-
Returns the current maximum number of rows in the results
- getMaxTime() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException
- getMaxTime() - Method in interface org.intermine.objectstore.ObjectStore
-
Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException
- getMaxTime() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException
- getMaxTime() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Get the maximum time a query may take before throwing an ObjectStoreQueryDurationException
- getMaxValues() - Method in class org.intermine.objectstore.ObjectStoreSummary
-
Return the configured maximum number of values to show in a dropdown.
- getMd5checksum() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getMessage() - Method in class org.intermine.api.bag.BagQuery
-
Return the message that was passed to the constructor.
- getMessage() - Method in class org.intermine.web.struts.ContactForm
-
- getMessage() - Method in exception org.intermine.webservice.client.exceptions.ResultException
- getMessage() - Method in exception org.intermine.webservice.client.exceptions.ServiceException
- getMessage() - Method in exception org.intermine.webservice.server.exceptions.ServiceException
- getMessageElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
-
- getMessageElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
-
- getMessageFormat() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
-
- getMessageFormat() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
-
- getMessageFormat() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
-
- getMethod() - Method in class org.intermine.bio.dataconversion.UniprotConfig.IdentifierConfig
-
- getMethodDescriptors() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
-
- getMethodDescriptors() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
-
- getMimeType() - Method in enum org.intermine.api.mines.ContentType
-
- getMin(String) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
-
Return the minimum coordinate of the given location
- getMin() - Method in class org.intermine.objectstore.query.ResultsInfo
-
Returns the minimum possible number of rows in the results.
- getMin() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary
-
- getMinBagTableSize() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Returns the cutoff value used to decide if a bag should be put in a table.
- getMinBagTableSize() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Returns the cutoff value used to decide if a bag should be put in a table.
- getMine(String) - Method in class org.intermine.api.mines.FriendlyMineManager
-
- getMineId() - Method in class org.intermine.webservice.server.lists.ListsServiceInput
-
- getMineResultsLink(String, String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
-
Get the link for a query that shows the results in a mine.
- getMineResultsLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
-
Get a link that takes the user to a results page in the originating mine.
- getMineResultsPath(String) - Method in class org.intermine.webservice.server.query.result.QueryResultLinkGenerator
-
Get the link path for a query that shows the results in a mine.
- getMineResultsPath(TemplateQuery, boolean) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
-
Get a link that takes the user to a results page in the originating mine.
- getMinimalPath() - Method in class org.intermine.pathquery.Node
-
- getMinParam() - Method in class org.intermine.objectstore.query.WidthBucketFunction
-
- getMinSize() - Method in class org.intermine.objectstore.query.ResultsBatches
-
Returns the current minimum number of rows in the results
- getMissingTables() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
-
Returns the Set of table names which are tables missing from the database.
- getMockIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a mock id resolver for unit test
- getMode() - Method in class org.intermine.sql.precompute.QueryOptimiserContext
-
Returns the optimiser mode of operation.
- getModel() - Method in interface org.intermine.api.API
-
- getModel() - Method in class org.intermine.api.InterMineAPI
-
- getModel() - Method in class org.intermine.api.mines.LocalMine
-
- getModel() - Method in interface org.intermine.api.mines.Mine
-
Get the main model associated with this application.
- getModel() - Method in class org.intermine.api.mines.RemoteMine
-
- getModel() - Method in class org.intermine.bio.dataconversion.ChadoProcessor
-
Return the Model of the target database.
- getModel() - Method in class org.intermine.bio.ontology.SequenceOntology
-
- getModel() - Method in class org.intermine.dataconversion.DataConverter
-
Return the data Model that was passed to the constructor.
- getModel() - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
-
Returns the Model used.
- getModel() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Return the metadata associated with this ObjectStore
- getModel() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
-
Returns the model.
- getModel() - Method in interface org.intermine.objectstore.ObjectStore
-
Return the metadata associated with this ObjectStore
- getModel() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Return the metadata associated with this ObjectStore
- getModel() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Return the metadata associated with this ObjectStore
- getModel() - Method in class org.intermine.pathquery.Path
-
Return the model that this path is created for.
- getModel() - Method in class org.intermine.pathquery.PathQuery
-
Returns the Model object stored in this object.
- getModel() - Method in class org.intermine.webservice.client.core.ServiceFactory
-
A convenience method to getting a model (used widely throughout the API).
- getModel() - Method in class org.intermine.webservice.client.services.ModelService
-
Returns the model used by the InterMine instance which the service is connected to.
- getModel() - Method in class org.intermine.xml.full.Item
-
Return the model that was passed to the constructor or set with setModel().
- getModelFromClasspath(String, Properties) - Static method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Read the Model from the classpath.
- getModelName() - Method in class org.intermine.task.ConverterTask
-
Return the model name
- getModelService() - Method in class org.intermine.webservice.client.core.ServiceFactory
-
Return a new ModelService for retrieving the data model.
- getModelXml() - Method in class org.intermine.webservice.client.services.ModelService
-
An method used internally to fetch the XML for the model from the server.
- getModifiableEditableConstraints() - Method in class org.intermine.template.TemplateQuery
-
Returns the list of all editable constraints.
- getMolecularWeight() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getMonkey() - Method in class org.intermine.web.struts.ContactForm
-
- getMostPopularTemplateOrder(Integer) - Method in class org.intermine.api.template.TemplateManager
-
Return the list of public templates ordered by rank descendant.
- getMostPopularTemplateOrder(String, String, Integer) - Method in class org.intermine.api.template.TemplateManager
-
Return the template list ordered by rank descendant for the user/sessionid specified
in the input
- getMouseIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a mouse id resolver
- getMouseIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a mouse id resolver
- getMouseIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a mouse id resolver
- getMrlv() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
-
Returns the MultiRowLaterValue corresponding to this object.
- getMRNA(String, Organism, Model) - Method in class org.intermine.bio.dataconversion.FlyBaseFeatureFastaLoaderTask
-
Create an MRNA with the given primaryIdentifier and organism or return null of MRNA is not in
the data model.
- getMultiValueAttribute() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Returs the value of multiValueAttribute
- getMultiValueAttribute() - Method in class org.intermine.web.struts.TemplateForm
-
Returns the multivalueattribute
- getMultiValueAttribute(String) - Method in class org.intermine.web.struts.TemplateForm
-
Returns the multivalueattribute given a key
- getMultiValues() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Returns the value collection if the constraint is a multivalue, otherwise return null.
- getMultivalues() - Method in class org.intermine.web.logic.template.ConstraintInput
-
Return multivalues
- getMultiValues() - Method in class org.intermine.web.struts.TemplateForm
-
Returns the multiValues
- getMultiValues(String) - Method in class org.intermine.web.struts.TemplateForm
-
Get a multi value
- getMultiValuesAsString() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
If the constraint is a multivalue, returns the value collection
represented as string separated by ', ', otherwise return an empty String.
- getName() - Method in class org.intermine.api.beans.ObjectDetails
-
- getName() - Method in class org.intermine.api.lucene.KeywordSearchFacet
-
user-friendly name
- getName() - Method in class org.intermine.api.lucene.KeywordSearchFacetData
-
name of the facet (displayed on page)
- getName() - Method in class org.intermine.api.mines.LocalMine
-
- getName() - Method in interface org.intermine.api.mines.Mine
-
- getName() - Method in class org.intermine.api.mines.RemoteMine
-
- getName() - Method in class org.intermine.api.profile.InterMineBag
-
Returns the value of name
- getName() - Method in class org.intermine.api.profile.InvalidBag
-
- getName() - Method in class org.intermine.api.profile.Profile
-
Return a first part of the username before the "@" sign (used in metabolicMine)
- getName() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
-
- getName() - Method in class org.intermine.api.profile.SavedQuery
-
Get the name of the saved query.
- getName() - Method in class org.intermine.api.profile.StorableBag
-
- getName() - Method in interface org.intermine.api.profile.Taggable
-
The name (or identifier) used as the primary key for storing this object.
- getName() - Method in exception org.intermine.api.query.BagNotFound
-
- getName() - Method in class org.intermine.api.results.Column
-
Get the name (title) of the column.
- getName() - Method in class org.intermine.api.tracker.AbstractTracker
-
Return the tracker's name
- getName() - Method in class org.intermine.api.tracker.KeySearchTracker
-
- getName() - Method in class org.intermine.api.tracker.ListTracker
-
Return the tracker's name
- getName() - Method in class org.intermine.api.tracker.LoginTracker
-
Return the tracker's name
- getName() - Method in class org.intermine.api.tracker.QueryTracker
-
Return the tracker's name
- getName() - Method in class org.intermine.api.tracker.TemplateTracker
-
Return the tracker's name
- getName() - Method in interface org.intermine.api.tracker.Tracker
-
Return the tracker's name
- getName() - Method in class org.intermine.bio.chado.ChadoCVTerm
-
Return the name of this term.
- getName() - Method in class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder
-
- getName() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getName() - Method in class org.intermine.bio.io.bed.BEDRecord
-
- getName() - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- getName() - Method in class org.intermine.bio.ontology.OboTerm
-
Get the name of this term.
- getName() - Method in class org.intermine.bio.ontology.OboTermSynonym
-
Get the synonym name.
- getName() - Method in class org.intermine.bio.ontology.OboTypeDefinition
-
- getName() - Method in class org.intermine.dataloader.Source
-
Getter for name.
- getName() - Method in class org.intermine.pathquery.LogicExpression.Variable
-
Get variable name.
- getName() - Method in class org.intermine.sql.Database
-
Gets the database name only, not the full URL.
- getName() - Method in class org.intermine.sql.precompute.PrecomputedTable
-
Gets the name of this PrecomputedTable
- getName() - Method in class org.intermine.sql.query.Field
-
Returns the name of the field.
- getName() - Method in class org.intermine.sql.query.Table
-
Returns the name of the table
- getName() - Method in class org.intermine.template.TemplateQuery
-
Get the query short name.
- getName() - Method in class org.intermine.web.logic.aspects.Aspect
-
Get the name of the data set.
- getName() - Method in class org.intermine.web.logic.aspects.AspectSource
-
Get the source name.
- getName() - Method in class org.intermine.web.logic.results.ReportObjectField
-
Get field name
- getName() - Method in class org.intermine.web.logic.template.TemplateResultInput
-
Returns template name.
- getName() - Method in class org.intermine.web.struts.ContactForm
-
- getName() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
-
- getName() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
-
- getName() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
-
- getName() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
-
- getName() - Method in class org.intermine.web.struts.TemplateForm
-
Get the template name.
- getName() - Method in class org.intermine.web.struts.TemplateSettingsForm
-
- getName() - Method in class org.intermine.webservice.client.lists.ItemList
-
Get the name of this list.
- getName() - Method in class org.intermine.webservice.client.widget.Widget
-
- getName() - Method in class org.intermine.xml.full.Attribute
-
Get the name of this field
- getName() - Method in class org.intermine.xml.full.Reference
-
Get the name of this field
- getName() - Method in class org.intermine.xml.full.ReferenceList
-
Get the name of this field.
- getNames() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the list of the Name field from the attributes of this record.
- getNameSource() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
-
- getNamespace() - Method in class org.intermine.bio.ontology.OboTerm
-
Get the namespace attribute.
- getNewBagName() - Method in class org.intermine.api.bag.operations.BagOperation
-
- getNewBagName() - Method in class org.intermine.web.struts.BagUploadConfirmForm
-
Get the bag name.
- getNewBagName() - Method in class org.intermine.web.struts.ModifyBagForm
-
Get the new bag name.
- getNewBagName() - Method in class org.intermine.web.struts.SaveBagForm
-
Gets the value of newBagName
- getNewBagType() - Method in class org.intermine.api.bag.operations.BagOperation
-
- getNewBagType() - Method in class org.intermine.api.bag.operations.Intersection
-
- getNewBagType() - Method in class org.intermine.api.bag.operations.RelativeComplement
-
- getNewBagType() - Method in class org.intermine.api.bag.operations.SymmetricDifference
-
- getNewBagType() - Method in class org.intermine.api.bag.operations.Union
-
- getNewBagType() - Method in class org.intermine.web.struts.TriageBagForm
-
Get the new bag name.
- getNewData() - Method in class org.intermine.dataloader.ObjectDescription
-
Returns the new data, which needs to be written back into the backing database.
- getNewId() - Method in class org.intermine.web.struts.oauth2.MigrationMapping
-
- getNewIds(InterMineObject, ObjectStore) - Method in interface org.intermine.api.bag.IdUpgrader
-
For the given object from an old ObjectStore, find the corresponding InterMineObjects in a
new ObjectStore.
- getNewIds(InterMineObject, ObjectStore) - Method in class org.intermine.web.bag.PkQueryIdUpgrader
-
For the given object from an old ObjectStore, find the corresponding InterMineObjects in a
new ObjectStore.
- getNewListType(ListInput) - Method in class org.intermine.webservice.server.lists.ListMakerService
-
Calculate the type of the new list.
- getNewListType(ListInput) - Method in class org.intermine.webservice.server.lists.ListOperationService
-
- getNewListType(ListInput) - Method in class org.intermine.webservice.server.lists.ListUploadService
-
- getNewObject() - Method in class org.intermine.api.bag.ConvertedObjectPair
-
Get the newObject that was passed to the constructor.
- getNewpassword() - Method in class org.intermine.web.struts.ChangePasswordForm
-
The new password
- getNewpassword() - Method in class org.intermine.web.struts.PasswordResetForm
-
Gets the value of newpassword.
- getNewpassword2() - Method in class org.intermine.web.struts.ChangePasswordForm
-
New password verification
- getNewpassword2() - Method in class org.intermine.web.struts.PasswordResetForm
-
Gets the value of newpassword2.
- getNewsPreview(String) - Static method in class org.intermine.dwr.AjaxServices
-
Work as a proxy for fetching remote file (RSS)
- getNewTemplateQuery() - Method in class org.intermine.api.profile.TemplateQueryUpdate
-
- getNewWriter() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Create an ObjectStoreWriter that writes into this ObjectStore.
- getNewWriter() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Create an ObjectStoreWriter that writes into this ObjectStore.
- getNewWriter() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Create an ObjectStoreWriter that writes into this ObjectStore.
- getNewWriter() - Method in interface org.intermine.objectstore.ObjectStore
-
Create an ObjectStoreWriter that writes into this ObjectStore.
- getNewWriter() - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Create an ObjectStoreWriter that writes into this ObjectStore.
- getNewWriter() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Create an ObjectStoreWriter that writes into this ObjectStore.
- getNextLine() - Method in class org.intermine.webservice.client.results.ResultSet
-
Get the next line of results.
- getNextLink(int) - Method in class org.intermine.web.tags.table.NavigationBarTag
-
- getNicerDisplayerName() - Method in class org.intermine.web.displayer.ReportDisplayer
-
A JSP wants a nice name to display while the Displayer is loading
- getNoConstraintsString() - Method in class org.intermine.pathquery.Path
-
Required for jsp
- getNonXrefs() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
used for testing
- getNoResultsMessage() - Method in class org.intermine.web.tags.table.TableTag
-
- getNormalInlineLists() - Method in class org.intermine.web.logic.results.ReportObject
-
- getNoseyObjectStore(ObjectStore) - Method in class org.intermine.dataloader.BatchingFetcher
-
Returns an ObjectStore layered on top of the given ObjectStore, which reports to this fetcher
which objects are being loaded.
- getNotAnalysed() - Method in class org.intermine.web.logic.widget.HTMLWidget
-
- getNotAnalysed() - Method in class org.intermine.web.logic.widget.Widget
-
- getNote() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the first value of the Note field from the attributes of this record.
- getNullAttributes(String) - Method in class org.intermine.objectstore.ObjectStoreSummary
-
Get a list of the attributes that, for a given class, are always null or empty.
- getNullConstraint() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Get the null/not null constraint value.
- getNullConstraint() - Method in class org.intermine.web.struts.TemplateForm
-
Get the nullConstraint
- getNullConstraint(String) - Method in class org.intermine.web.struts.TemplateForm
-
Get a nullConstraint
- getNullReferencesAndCollections(String) - Method in class org.intermine.objectstore.ObjectStoreSummary
-
Get a list of the reference and collection names that, for a given class, are always
null or empty.
- getNumberOfBins() - Static method in class org.intermine.api.query.MainHelper.SummaryConfig
-
Returns the number of bins to split a histogram into.
- getNumberOfMainTitlesToShow() - Method in class org.intermine.web.logic.config.HeaderConfigTitle
-
- getNumberOfTableRowsToShow() - Method in class org.intermine.web.logic.results.ReportObject
-
The said function will resolve the maximum number of rows to show (in Collections)
from webProperties.
- getNumberOpt() - Method in class org.intermine.web.struts.WidgetForm
-
- getNumericSummary(PathQuery, String) - Method in class org.intermine.webservice.client.services.QueryService
-
Get a summary for the values in column of a query.
- getOAuth2Providers(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Get the set of accepted Open-ID providers.
- getObject() - Method in class org.intermine.api.lucene.KeywordSearchHit
-
object
- getObject() - Method in interface org.intermine.api.results.ResultCell
-
- getObject() - Method in class org.intermine.api.results.ResultElement
-
Return the Object contained in this result element.
- getoBJECT() - Method in interface org.intermine.model.InterMineObject
-
Returns the NotXml serialised version of this object.
- getObject() - Method in class org.intermine.objectstore.proxy.ProxyReference
-
Gets the real object from the database.
- getoBJECT() - Method in class org.intermine.objectstore.proxy.ProxyReference
-
Returns the NotXml serialised version of this object.
- getObject() - Method in class org.intermine.objectstore.query.ContainsConstraint
-
Returns the InterMineObject of the constraint.
- getObject() - Method in class org.intermine.web.logic.config.InlineListObject
-
Fetch the InterMine object (if needed)
- getObject() - Method in class org.intermine.web.logic.results.DisplayReference
-
Get the referenced object
- getObject() - Method in class org.intermine.web.logic.results.ReportObject
-
Get InterMine object
- getObject() - Method in class org.intermine.web.logic.TreeNode
-
Get the Object
- getObject() - Method in class org.intermine.web.search.KeywordSearchResult
-
returns original intermine object
- getObject() - Method in class org.intermine.webservice.server.core.TableCell
-
- getObjectByExample(T, Set<String>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
- getObjectByExample(T, Set<String>) - Method in interface org.intermine.objectstore.ObjectStore
-
Return an object from the objectstore that has the fields mentioned in the list set to the
same values as the fields in the provided example object.
- getObjectByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
- getObjectByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Return an object from the objectstore that has the fields mentioned in the list set to the
same values as the fields in the provided example object.
- getObjectByExample(T, Set<String>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
-
- getObjectById(Integer) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Search database for object matching the given object id
- getObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Search database for object matching the given object id and class
- getObjectById(Integer) - Method in interface org.intermine.objectstore.ObjectStore
-
Get an object from the ObjectStore by giving an ID.
- getObjectById(Integer, Class<? extends InterMineObject>) - Method in interface org.intermine.objectstore.ObjectStore
-
Get an object from the ObjectStore by giving an ID and a hint of the Class of the object.
- getObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Get an object from the ObjectStore by giving an ID.
- getObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Get an object from the ObjectStore by giving an ID and a hint of the Class of the object.
- getObjectById(Integer) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Get an object from the ObjectStore by giving an ID.
- getObjectById(Integer, Class<? extends InterMineObject>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Get an object from the ObjectStore by giving an ID and a hint of the Class of the object.
- getObjectHits - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
- getObjectId() - Method in class org.intermine.web.logic.results.InlineResultsTableRow
-
Used from JSP
- getObjectId() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
-
Get the object id for this trail element.
- getObjectIds(BrowseHit[]) - Static method in class org.intermine.api.lucene.KeywordSearch
-
- getObjectOps - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
- getObjectPrefetches - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
- getObjects() - Method in class org.intermine.api.beans.PartnerLink
-
- getObjects(InterMineAPI, Set<Integer>) - Static method in class org.intermine.api.data.Objects
-
Resolve a set of ids to mapping from ID to object.
- getObjects() - Method in class org.intermine.webservice.client.results.JSONResult
-
- getObjectsByExample(T, Set<String>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
- getObjectsByExample(T, Set<String>) - Method in interface org.intermine.objectstore.ObjectStore
-
Return an object from the objectstore that has the fields mentioned in the list set to the
same values as the fields in the provided example object.
- getObjectsByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
- getObjectsByExample(T, Set<String>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
- getObjectsByExample(T, Set<String>) - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
-
- getObjectsByIds(Collection<Integer>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Get an objects from the ObjectStore that have the IDs in the ids colection
- getObjectsByIds(Collection<Integer>) - Method in interface org.intermine.objectstore.ObjectStore
-
Get an objects from the ObjectStore that have the IDs in the ids colection
- getObjectsByIds(Collection<Integer>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Get an objects from the ObjectStore that have the IDs in the ids colection
- getObjectsByIds(Collection<Integer>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Get an objects from the ObjectStore that have the IDs in the ids colection
- getObjectStore() - Method in interface org.intermine.api.API
-
- getObjectStore() - Method in class org.intermine.api.InterMineAPI
-
- getObjectStore() - Static method in class org.intermine.api.query.PathQueryAPI
-
Returns the production ObjectStore configured in webapp.os.alias.
- getObjectStore() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Retrieve this Writer's ObjectStore.
- getObjectStore() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Retrieve this Writer's ObjectStore.
- getObjectStore() - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer
-
Returns the ObjectStore that this ParallelPrecomputer uses.
- getObjectStore(String) - Static method in class org.intermine.objectstore.ObjectStoreFactory
-
Return an ObjectStore configured using properties
- getObjectStore() - Method in interface org.intermine.objectstore.ObjectStoreWriter
-
Retrieve this Writer's ObjectStore.
- getObjectStore() - Method in interface org.intermine.objectstore.proxy.Lazy
-
Returns the ObjectStore that this lazy object will use
- getObjectStore() - Method in class org.intermine.objectstore.proxy.ProxyCollection
-
Returns the ObjectStore that this proxy will use
- getObjectStore() - Method in class org.intermine.objectstore.proxy.ProxyReference
-
Returns the ObjectStore that this proxy will use
- getObjectStore() - Method in class org.intermine.objectstore.query.ClobAccess
-
Returns the ObjectStore that this object will use to access data.
- getObjectStore() - Method in class org.intermine.objectstore.query.PendingClob
-
Returns the ObjectStore that this object will use to access data.
- getObjectStore() - Method in class org.intermine.objectstore.query.Results
-
Returns the ObjectStore that this Results object will use
- getObjectStore() - Method in class org.intermine.objectstore.query.ResultsBatches
-
Returns the ObjectStore that this ResultsBatches object will use
- getObjectStoreSummary() - Method in interface org.intermine.api.API
-
- getObjectStoreSummary() - Method in class org.intermine.api.InterMineAPI
-
- getObjectStoreWriter() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Returns the underlying ObjectStoreWriter.
- getObjectStoreWriter(String) - Static method in class org.intermine.objectstore.ObjectStoreWriterFactory
-
Return an ObjectStoreWriter configured using properties file
- getObjectStoreWriter() - Method in class org.intermine.postprocess.PostProcessor
-
Return the ObjectStoreWriter that was passed to the constructor.
- getObjectSummaryFields() - Method in class org.intermine.web.logic.results.ReportObject
-
A listing of object fields as pieced together from the various ReportObject methods
- getObjectTagNames(String, String, String) - Method in class org.intermine.api.profile.TagManager
-
Returns names of tagged tags for specified object.
- getObjectTagNames(Taggable, Profile) - Method in class org.intermine.api.profile.TagManager
-
Returns names of tagged tags for specified object.
- getObjectTags(Taggable, Profile) - Method in class org.intermine.api.profile.TagManager
-
Get the tags for a specific object.
- getObjectTags(String, String) - Static method in class org.intermine.dwr.AjaxServices
-
Returns all tags by which is specified object tagged.
- getOboRelations() - Method in class org.intermine.bio.ontology.OboParser
-
- getOboTerms() - Method in class org.intermine.bio.ontology.OboParser
-
- getOfficialName(Connection, Integer) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the rows needed for data from the applied_protocol_data table.
- getOffset() - Method in class org.intermine.objectstore.query.ClobAccess
-
Return the offset into the underlying clob that this object is using.
- getOffset() - Method in class org.intermine.objectstore.query.PendingClob
-
Return the offset into the underlying clob that this object is using.
- getOffset() - Method in class org.intermine.sql.precompute.LimitOffsetQuery
-
Getter for offset.
- getOffset() - Method in class org.intermine.sql.query.Query
-
Gets the OFFSET number for this query.
- getOffsetConstraint(Query, QueryOrderable, Object, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Create a constraint to add to the main query to deal with offset - this is based on
the first element in the order by (field) and a given value (x).
- getOldId() - Method in class org.intermine.web.struts.oauth2.MigrationMapping
-
- getOldObject() - Method in class org.intermine.api.bag.ConvertedObjectPair
-
Get the objObject that was passed to the constructor.
- getOldpassword() - Method in class org.intermine.web.struts.ChangePasswordForm
-
The old password
- getOnClick() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
-
- getOntology(DataConverter) - Static method in class org.intermine.bio.util.BioConverterUtil
-
Create and store ontology object.
- getOntologyTerm() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the first value of the OntologyTerm field from the attributes of this record.
- getOp() - Method in class org.intermine.objectstore.query.Constraint
-
Get op of constraint
- getOp() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
-
Returns the op of this combination.
- getOp() - Method in class org.intermine.pathquery.PathConstraint
-
Returns the operation that this constraint performs.
- getOp() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
-
Get a string representation of the constraint operation.
- getOpened() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
-
Returns true if disclosure is opened else false.
- getOpenIdProviders(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Get the set of accepted Open-ID providers.
- getOperands() - Method in class org.intermine.sql.query.Function
-
Returns the List of operands of this function.
- getOperation() - Method in class org.intermine.objectstore.query.QueryExpression
-
Returns the operation.
- getOperation() - Method in class org.intermine.objectstore.query.QueryFunction
-
Returns the operation of the function.
- getOperation() - Method in class org.intermine.sql.query.Constraint
-
Returns the operation of the constraint.
- getOperation() - Method in class org.intermine.sql.query.Function
-
Returns the operation of the function.
- getOperation() - Method in class org.intermine.template.TemplateValue
-
- getOperation() - Method in class org.intermine.webservice.client.template.TemplateParameter
-
- getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListDifferenceService
-
- getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListIntersectionService
-
- getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListOperationService
-
Get the BagOperation that will create the list.
- getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListSubtractionService
-
- getOperation(ListInput) - Method in class org.intermine.webservice.server.lists.ListUnionService
-
- getOperationButton() - Method in class org.intermine.web.struts.SaveBagForm
-
- getOperationCode() - Method in class org.intermine.api.bag.operations.BagOperation
-
- getOperationCode() - Method in class org.intermine.api.bag.operations.Intersection
-
- getOperationCode() - Method in class org.intermine.api.bag.operations.RelativeComplement
-
- getOperationCode() - Method in class org.intermine.api.bag.operations.SymmetricDifference
-
- getOperationCode() - Method in class org.intermine.api.bag.operations.Union
-
- getOperator() - Method in class org.intermine.pathquery.LogicExpression.And
-
Override to provide text symbol for this operator.
- getOperator() - Method in class org.intermine.pathquery.LogicExpression.Operator
-
Override to provide text symbol for this operator.
- getOperator() - Method in class org.intermine.pathquery.LogicExpression.Or
-
Override to provide text symbol for this operator.
- getOperator() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Get the operator.
- getOptimised() - Method in class org.intermine.sql.precompute.OptimiserCacheLine
-
Gets the optimised query (minus the LIMIT and OFFSET) from this cache line.
- getOptionalParameter(String, String) - Method in class org.intermine.webservice.server.WebService
-
Get a parameter this service deems to be optional, or the default value.
- getOptionalParameter(String) - Method in class org.intermine.webservice.server.WebService
-
Get a parameter this service deems to be optional, or null.
- getOptions() - Method in class org.intermine.web.task.IssueTokenTask
-
- getOptions() - Method in class org.intermine.web.task.KeyStoreTask
-
Get the options as configured for this task
- getOptionsTileName() - Method in class org.intermine.web.logic.config.TableExportConfig
-
Get the optionsTileName of this TableExportConfig - ie. the tile to be inserted into the
export options page for this type of export.
- getOrderBy() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- getOrderBy() - Method in class org.intermine.objectstore.query.Query
-
Gets the ORDER BY clause of this Query
- getOrderBy() - Method in class org.intermine.pathquery.PathQuery
-
Returns the current order by list.
- getOrderBy() - Method in class org.intermine.sql.query.Query
-
Gets the list of fields forming the ORDER BY clause of this query.
- getOrderByAlias() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- getOrderByField() - Method in class org.intermine.sql.precompute.PrecomputedTable
-
Returns the name of the order by field, if it exists.
- getOrderPath() - Method in class org.intermine.pathquery.OrderElement
-
Returns the path of this OrderElement.
- getOrganism(String) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
-
The Organism item created from the taxon id passed to the constructor.
- getOrganism(String) - Method in class org.intermine.bio.dataconversion.BioFileConverter
-
The Organism item created from the taxon id passed to the constructor.
- getOrganism(Sequence) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
Get and store() the Organism object to reference when creating new objects.
- getOrganism() - Method in class org.intermine.bio.dataconversion.GFF3Converter
-
Return the organism Item created for this GFF3Converter from the organism abbreviation passed
to the constructor.
- getOrganism() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Return the organism Item set by setOrganism()
- getOrganism(Sequence) - Method in class org.intermine.bio.dataconversion.UniProtFastaLoaderTask
-
Get and store() the Organism object to reference when creating new objects.
- getOrganismConstraint() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return some SQL that can be included in the WHERE part of query that restricts features
by organism.
- getOrganismConstraint() - Method in class org.intermine.bio.dataconversion.StockProcessor
-
Return some SQL that can be included in the WHERE part of query that restricts features
by organism.
- getOrganismDataByAbbreviation(String) - Method in class org.intermine.bio.util.OrganismRepository
-
Look up OrganismData objects by abbreviation, abbreviations are not case sensitive.
- getOrganismDataByFullName(String) - Method in class org.intermine.bio.util.OrganismRepository
-
Look up OrganismData objects by a full name that is genus species.
- getOrganismDataByGenusSpecies(String, String) - Method in class org.intermine.bio.util.OrganismRepository
-
Look up OrganismData objects by genus and species - both must match.
- getOrganismDataByShortName(String) - Method in class org.intermine.bio.util.OrganismRepository
-
Look up OrganismData objects by shortName, short names are case sensitive.
- getOrganismDataByTaxon(int) - Method in class org.intermine.bio.util.OrganismRepository
-
Look up OrganismData objects by taxon id.
- getOrganismDataByTaxonInternal(int) - Method in class org.intermine.bio.util.OrganismRepository
-
Look up OrganismData objects by taxon id.
- getOrganismDataByUniprot(String) - Static method in class org.intermine.bio.util.OrganismRepository
-
Look up OrganismData objects by Uniprot abbreviation, eg HUMAN or DROME.
- getOrganismItem(int) - Method in class org.intermine.bio.dataconversion.BioDBConverter
-
The Organism item created from the taxon id passed to the constructor.
- getOrganismRepository() - Static method in class org.intermine.bio.util.OrganismRepository
-
Return an OrganismRepository created from a properties file in the class path.
- getOrganisms(ObjectStore) - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
-
Retrieve the organisms to be updated
- getOrganisms(ObjectStore, String, List<Integer>, boolean) - Static method in class org.intermine.bio.util.BioUtil
-
For a bag of objects, returns a list of organisms
- getOrganisms(ObjectStore, String, List<Integer>, boolean, String) - Static method in class org.intermine.bio.util.BioUtil
-
For a bag of objects, returns a list of organisms.
- getOrganismsToProcess() - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
-
Return the OrganismData objects for the organisms listed in the source configuration.
- getOrig() - Method in class org.intermine.dataloader.ObjectDescription
-
Returns the original data, as reflected in the backing database.
- getOrigin() - Method in class org.intermine.api.search.OriginatingEvent
-
Get the web searchable involved in this event.
- getOriginal() - Method in class org.intermine.sql.precompute.OptimiserCacheLine
-
Returns the original SQL string.
- getOriginalSql() - Method in class org.intermine.sql.precompute.PrecomputedTable
-
Returns the original SQL text stored in the index for this PrecomputedTable
- getOriginalValue() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
- getOrigType() - Method in class org.intermine.web.logic.query.MetadataNode
-
Returns the type of this node if it did not have a subclass constraint.
- getOs() - Method in class org.intermine.objectstore.query.ClobAccess
-
Returns the ObjectStore that this object uses.
- getOsb() - Method in class org.intermine.api.profile.InterMineBag
-
Returns the ObjectStoreBag, so that elements can be added and removed.
- getOsb() - Method in class org.intermine.api.profile.InvalidBag
-
- getOsb() - Method in class org.intermine.api.profile.StorableBag
-
Return a reference to the object store bag contained in the production database.
- getOsb() - Method in class org.intermine.objectstore.query.BagConstraint
-
Get the ObjectStoreBag.
- getOsb() - Method in class org.intermine.objectstore.query.QueryClassBag
-
Returns the ObjectStoreBag.
- getOsName() - Method in class org.intermine.task.ConverterTask
-
Return the object store alias set by setOsName().
- getOuterInSummary() - Method in class org.intermine.web.logic.config.FieldConfig
-
- getOuterJoinGroup() - Method in class org.intermine.pathquery.Node
-
Returns a String describing the outer join group that this Node is in.
- getOuterJoinGroup(String) - Static method in class org.intermine.pathquery.Node
-
Returns a String describing the outer join group that the given path string is in.
- getOuterJoinGroup(String) - Method in class org.intermine.pathquery.PathQuery
-
Returns the outer join group that the given path is in.
- getOuterJoinGroups() - Method in class org.intermine.pathquery.PathQuery
-
Returns the outer join groups map for this query, if the query verifies correctly.
- getOuterJoinStatus(String) - Method in class org.intermine.pathquery.PathQuery
-
Returns the outer join status of the last part of a given path in this query.
- getOuterJoinStatus() - Method in class org.intermine.pathquery.PathQuery
-
Returns an unmodifiable Map which is a copy of the current outer join status of this query at
the time of execution of this method.
- getOuterMap() - Method in class org.intermine.pathquery.PathQuery
-
Returns a Map from path to TRUE for all paths that are outer joined.
- getOutputInfo(String) - Method in interface org.intermine.web.logic.widget.CorrectionCoefficient
-
Return the key value pairs to put in the webservice result
- getOutsideOptions() - Method in class org.intermine.api.query.range.AbstractHelper
-
By default the OUTSIDE options are the negation of the WITHIN options, with the
right and left fields swapped.
- getOutwardIndirectionColumnName(CollectionDescriptor, int) - Static method in class org.intermine.sql.DatabaseUtil
-
Creates a column name for the "outward" key of a many-to-many collection descriptor.
- getOverlapsOptions() - Method in class org.intermine.api.query.range.AbstractHelper
-
By default the OVERLAPS options are the same as the WITHIN options with the right
and left fields swapped.
- getPackageName() - Method in class org.intermine.objectstore.query.iql.IqlQuery
-
Get the package name
- getPage() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Get the page index.
- getPagedTable() - Method in class org.intermine.web.logic.query.PageTableQueryMonitor
-
Return the PagedTable that was passed to the constructor.
- getPagedTable(HttpServletRequest, HttpSession) - Method in class org.intermine.web.struts.TableExportAction
-
- getPageLink(int) - Method in class org.intermine.web.tags.table.NavigationBarTag
-
- getPageName() - Method in class org.intermine.web.struts.ModifyBagForm
-
- getPageName() - Method in class org.intermine.web.struts.ModifyTemplateForm
-
- getPageSize() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Get the page size of the current page
- getPageSize() - Method in class org.intermine.web.struts.ChangeTableSizeForm
-
Get the page size
- getPageSize() - Method in class org.intermine.web.tags.table.NavigationBarTag
-
- getParam() - Method in class org.intermine.objectstore.query.QueryFunction
-
Returns the QueryEvaluable of the function.
- getParam2() - Method in class org.intermine.objectstore.query.QueryFunction
-
Returns the second evaluable, where these is one.
- getParameter(String) - Method in interface org.intermine.webservice.client.core.Request
-
Use only if you are sure, that the parameter has
only one value else use getParameterValues method.
- getParameter(String) - Method in class org.intermine.webservice.client.core.RequestImpl
-
Use only if you are sure, that the parameter has
only one value else use getParameterValues method.
- getParameterJson() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Get the parameters for this displayer as a JSONObject
- getParameterMap() - Method in interface org.intermine.webservice.client.core.Request
-
Returns all parameters as an unmodifiable map.
- getParameterMap() - Method in class org.intermine.webservice.client.core.RequestImpl
-
Returns all parameters as an unmodifiable map.
- getParameterName() - Method in class org.intermine.web.logic.template.ConstraintInput
-
- getParameterNames() - Method in interface org.intermine.webservice.client.core.Request
-
- getParameterNames() - Method in class org.intermine.webservice.client.core.RequestImpl
- getParameters() - Method in class org.intermine.objectstore.query.iql.IqlQuery
-
Get the parameters
- getParameters() - Method in class org.intermine.web.util.AttributeLinkURL
-
- getParameterString() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
A JSON string representing custom parameters for this displayer.
- getParameterValues(String) - Method in interface org.intermine.webservice.client.core.Request
-
- getParameterValues(String) - Method in class org.intermine.webservice.client.core.RequestImpl
- getParams() - Method in class org.intermine.web.logic.config.Displayer
-
Return the parameters stored in this Displayer.
- getParent() - Method in class org.intermine.objectstore.query.OverlapRange
-
Returns the parent parameter.
- getParent() - Method in class org.intermine.pathquery.Node
-
Get the parent node.
- getParent() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
-
Returns a new DisplayPath that represents the parent path, or null if this path is just a
root class.
- getParentId() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
-
Get parentId value
- getParents() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the list of the Parent field from the attributes of this record.
- getParentTermId() - Method in class org.intermine.bio.ontology.OboRelation
-
- getParentType() - Method in class org.intermine.pathquery.Node
-
Type of parent node.
- getParentType() - Method in class org.intermine.web.logic.results.InlineResultsTable
-
Get the parent's type
- getPartialString(List<String>) - Method in class org.intermine.pathquery.LogicExpression
-
Produce an expression for this branch of the tree displaying only the children containing
the variable in input
- getParts() - Method in class org.intermine.webservice.client.core.MultiPartRequest
-
- getPassword() - Method in class org.intermine.api.profile.Profile
-
Get the value of password
- getPassword(String) - Method in class org.intermine.api.profile.ProfileManager
-
Get a user's password
A check should be made prior to this call to ensure a Profile exists
- getPassword() - Method in class org.intermine.sql.Database
-
Gets the password for this Database
- getPassword() - Method in class org.intermine.web.struts.CreateAccountForm
-
- getPassword() - Method in class org.intermine.web.struts.LoginForm
-
Gets the value of password
- getPassword() - Method in class org.intermine.webservice.server.WebServiceInput
-
- getPassword2() - Method in class org.intermine.web.struts.CreateAccountForm
-
- getPath() - Method in class org.intermine.api.results.Column
-
Get the Path set by setPath().
- getPath() - Method in interface org.intermine.api.results.ResultCell
-
- getPath() - Method in class org.intermine.api.results.ResultElement
-
- getPath() - Method in class org.intermine.pathquery.PathConstraint
-
Returns the path that this constraint is attached to.
- getPath() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
-
The path that should be in the title, with style removed.
- getPath() - Method in class org.intermine.web.logic.config.InlineListConfig
-
- getPath() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Get a representation of the path that is being constraint.
- getPath() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
-
Return the underlying path object.
- getPath() - Method in class org.intermine.web.logic.results.InlineList
-
- getPath() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Gets the value of path
- getPath() - Method in class org.intermine.webservice.server.core.TableCell
-
- getPathConstraint() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
-
Returns the pathConstraint based on the enrichmentIdentifier will be applied on the pathQUery
- getPathConstraints() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- getPathConstraintsForView() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- getPathId() - Method in class org.intermine.web.logic.template.ConstraintInput
-
- getPathId() - Method in class org.intermine.webservice.client.template.TemplateParameter
-
- getPathQuery() - Method in class org.intermine.api.profile.SavedQuery
-
Get the saved PathQuery.
- getPathQuery() - Method in class org.intermine.api.results.WebResults
-
- getPathQuery() - Method in interface org.intermine.api.results.WebTable
-
Get the PathQuery associated with this WebTable
- getPathQuery() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
-
- getPathQuery() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
- getPathQuery() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
-
Returns the pathquery based on the views set in config file and the bag constraint
Executed when the user selects any item in the matches column in the enrichment widget.
- getPathQuery() - Method in class org.intermine.web.logic.widget.GraphWidget
-
Returns the pathquery based on the views set in config file and the bag constraint.
- getPathQuery() - Method in class org.intermine.web.logic.widget.HTMLWidget
-
- getPathQuery() - Method in class org.intermine.web.logic.widget.TableWidget
-
- getPathQuery() - Method in class org.intermine.web.logic.widget.Widget
-
Return the PathQuery generated dynamically by the attribute views in the configuration file
- getPathQueryExecutor(Profile) - Method in interface org.intermine.api.API
-
- getPathQueryExecutor() - Method in class org.intermine.api.InterMineAPI
-
- getPathQueryExecutor(Profile) - Method in class org.intermine.api.InterMineAPI
-
- getPathQueryExecutor() - Static method in class org.intermine.api.query.PathQueryAPI
-
Returns a PathQueryExecutor, using properties.
- getPathQueryForMatches() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
-
Returns the pathquery based on the startClassDisplay, constraintsForView set in config file
and the bag constraint
Executed when the user click on the matches column in the enrichment widget.
- getPathsString() - Method in class org.intermine.web.struts.TableExportForm
-
Get the paths string in the format: "Class.field Class.field2 Class.ref.field"
- getPathString() - Method in class org.intermine.pathquery.Node
-
Gets the String value of pathString of this node (eg.
- getPathString() - Method in exception org.intermine.pathquery.PathException
-
Return the path String that was passed to the constructor.
- getPathString() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
-
Returns the full path string for this path.
- getPathString() - Method in class org.intermine.web.logic.results.ReportObjectField
-
Get a path string to fetch field descriptions
- getPathStrings() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
Comma separated list of path strings to appear in the widget, ie Employee.firstName,
Employee.lastName
- getPathToBagQueryResult() - Method in class org.intermine.api.results.WebResults
-
Returns the pathToBagQueryResult Map.
- getPathToBagQueryResult() - Method in interface org.intermine.api.results.WebTable
-
Returns the pathToBagQueryResult Map.
- getPathToIndex() - Method in class org.intermine.api.results.WebResults
-
Create a map from string paths to index of QueryNodes in the ObjectStore query
- getPathToQueryNode() - Method in class org.intermine.api.results.WebResults
-
Returns the pathToQueryNode Map.
- getPathUpdated(String, Map<String, String>, Map<String, String>) - Method in class org.intermine.api.profile.PathQueryUpdate
-
Update the path given in input with the renamed classes and fields
- getPathWithoutSubClass(Model, String) - Static method in class org.intermine.web.logic.widget.config.WidgetConfigUtil
-
- getPerlWSModuleVer() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
-
- getPermanentBaseURL() - Method in class org.intermine.web.util.URLGenerator
-
Generates base url.
- getPermission(String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
-
Get the level of permission granted by an access token.
- getPermission(PermanentToken, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
-
- getPermission(String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
-
Authenticate a user using username/password credentials.
- getPermission() - Method in class org.intermine.webservice.server.WebService
-
Return the permission object representing the authorisation state of the
request.
- getPhase() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the phase field of this record.
- getPlacement() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Get the data category name under which this displayer should appear.
- getPlatform() - Method in class org.intermine.sql.Database
-
Gets the platform of this Database
- getPoints() - Method in class org.intermine.web.search.KeywordSearchResult
-
return points
- getPopularTemplatesByAspect(String, Integer) - Method in class org.intermine.api.template.TemplateManager
-
Return the template list for a particular aspect given in input, ordered by rank descendant
- getPopularTemplatesByAspect(String, Integer, String, String) - Method in class org.intermine.api.template.TemplateManager
-
Return the template list for a particular aspect, ordered by rank descendant for
the user/sessionid specified in the input
- getPopulatedTemplate(TemplateQuery, Map<String, List<TemplateValue>>) - Static method in class org.intermine.api.template.TemplatePopulator
-
Given a template and a map of values for editable constraints on each editable node create
a copy of the template query with the values filled in.
- getPopulationBagName() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
-
Get the bag's name for reference population
- getPopulationInfo() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
-
Return a population info instance contanining the population size,
N (In our example this is the total number of companies, or possibly
the total number of companies that have at least one Department)
and the average length of the genes in the whole population.
- getPopulationInfo() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
-
- getPopulationQuery(boolean) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
-
- getPossibleValues(ApiTemplate, String) - Method in class org.intermine.api.template.TemplateSummariser
-
Returns the possible values that a particular path in a template query can take,
for dropdowns on template forms.
- getPossibleValues(ApiTemplate) - Method in class org.intermine.api.template.TemplateSummariser
-
Returns a Map of the possible values for editable nodes on a template query.
- getPossibleValues() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Values to populate a dropdown for the path if possible values are available.
- getPrecomputedSummarisedInfo(Profile, HttpSession, HttpServletRequest) - Static method in class org.intermine.web.struts.MyMineController
-
Retrieve the information about precomputed and summarised templates for the
given profile, and store it into the request
- getPrecomputedTables() - Method in class org.intermine.sql.precompute.PrecomputedTableManager
-
Get all the precomputed tables in the underlying database.
- getPrecomputeQuery(TemplateQuery, List) - Static method in class org.intermine.api.template.TemplatePrecomputeHelper
-
Get an ObjectStore query to precompute this template - remove editable constraints
and add fields to select list if necessary.
- getPrecomputeQuery(TemplateQuery, List<? super QueryNode>, String) - Static method in class org.intermine.api.template.TemplatePrecomputeHelper
-
Get an ObjectStore query to precompute this template - remove editable constraints
and add fields to select list if necessary.
- getPrecomputeQuery(TemplateQuery, List<? super QueryNode>, String, InterMineAPI) - Static method in class org.intermine.api.template.TemplatePrecomputeHelper
-
Get an ObjectStore query to precompute this template - remove editable constraints
and add fields to select list if necessary.
- getPrecomputer(ObjectStoreInterMineImpl) - Method in class org.intermine.task.PrecomputeTask
-
Create a ParallelPrecomputer.
- getPrecomputeTemplateQueries() - Method in class org.intermine.web.task.PrecomputeTemplatesTask
-
Get the super user's public templates
- getPreDefaultBagQueries(String) - Method in class org.intermine.api.bag.BagQueryConfig
-
Return a List of BagQuerys for the given type that should be run before the
default query
- getPreferences(Profile) - Method in class org.intermine.api.profile.PreferencesManager
-
- getPreferences() - Method in class org.intermine.api.profile.Profile
-
Get the object representing the preferences of this user.
- getPreferences(Profile) - Method in class org.intermine.api.profile.ProfileManager
-
Get the preferences for a profile.
- getPrefix() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
-
- getPrefix() - Method in class org.intermine.pathquery.Node
-
Gets the value of prefix
- getPrefix() - Method in class org.intermine.pathquery.Path
-
Return a Path object that represents the prefix of this path, ie this Path without the
last element.
- getPrefix() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
-
A prefix that may be an HTML tag to appear before this part in the title.
- getPrefix() - Method in class org.intermine.web.logic.results.InlineList
-
- getPrefixes() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
used for testing
- getPreviousLink(int) - Method in class org.intermine.web.tags.table.NavigationBarTag
-
- getPrimaryAccession() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getPrimaryIdentifier() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getPrimaryKeys(ClassDescriptor, Source, ObjectStore) - Static method in class org.intermine.dataloader.DataLoaderHelper
-
Return a Set of PrimaryKeys relevant to a given Source for a ClassDescriptor.
- getPrintWriterForClient(HttpServletRequest, OutputStream) - Static method in class org.intermine.web.logic.export.http.HttpExportUtil
-
- getPriorities(Class<? extends FastPathObject>, String) - Method in class org.intermine.dataloader.PriorityConfig
-
Returns a List of data source names representing the priority for a given class and
fieldname pair.
- getProblems() - Method in exception org.intermine.api.query.codegen.InvalidQueryException
-
- getProcessingInstruction() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
-
- getProcessingInstruction() - Method in class org.intermine.webservice.server.output.XMLFormatter
-
- getProcessor() - Method in class org.intermine.webservice.server.widget.EnrichmentWidgetResultService
-
- getProcessor() - Method in class org.intermine.webservice.server.widget.GraphService
-
- getProcessor() - Method in class org.intermine.webservice.server.widget.TableWidgetService
-
- getProcessor() - Method in class org.intermine.webservice.server.widget.WidgetService
-
- getProductionObjectStore() - Method in class org.intermine.api.profile.ProfileManager
-
Return the ObjectStore that was passed to the constructor.
- getProfile() - Method in class org.intermine.api.bag.operations.BagOperation
-
- getProfile() - Method in class org.intermine.api.profile.ProfileManager.ApiPermission
-
- getProfile(String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
-
Get a user's Profile using a username, password and the classKeys.
- getProfile(String, String) - Method in class org.intermine.api.profile.ProfileManager
-
Get a user's Profile using a username and password.
- getProfile(String) - Method in class org.intermine.api.profile.ProfileManager
-
Get a user's Profile using a username
- getProfile(int) - Method in class org.intermine.api.profile.ProfileManager
-
Get a user's Profile using an ID
- getProfile(String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
-
Get a user's Profile using a username
- getProfile() - Static method in class org.intermine.api.query.PathQueryAPI
-
Returns the superuser Profile.
- getProfile() - Method in class org.intermine.api.search.SearchRepository
-
Get the profile that this repository belongs to.
- getProfile(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Returns user profile saved in session.
- getProfile() - Method in class org.intermine.webservice.server.user.DeletionToken
-
- getProfileId() - Method in class org.intermine.api.profile.StorableBag
-
- getProfileManager() - Method in interface org.intermine.api.API
-
- getProfileManager() - Method in class org.intermine.api.InterMineAPI
-
- getProfileManager() - Method in class org.intermine.api.profile.Profile
-
Return the ProfileManager that was passed to the constructor.
- getProfileManager() - Static method in class org.intermine.api.query.PathQueryAPI
-
Returns the ProfileManager configured in webapp.userprofile.os.alias.
- getProfileObjectStoreWriter() - Method in class org.intermine.api.profile.ProfileManager
-
Return the userprofile ObjectStoreWriter that was passed to the constructor.
- getProfileUserName(int) - Method in class org.intermine.api.profile.ProfileManager
-
Return the name of the user with the given internal DB id.
- getProfileUserNames() - Method in class org.intermine.api.profile.ProfileManager
-
Return a List of the usernames in all of the stored profiles.
- getProjects(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the project name.
- getProjectTitle() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
-
- getProperties() - Static method in class org.intermine.api.query.PathQueryAPI
-
Returns the properties accessible for this system.
- getProperties() - Static method in class org.intermine.util.PropertiesUtil
-
Returns all InterMine properties
- getProperties() - Method in class org.intermine.webservice.client.results.Item
-
Return a view of the properties in this row.
- getPropertiesFileName(String) - Static method in class org.intermine.task.PrecomputeTask
-
Return the name of the properties file we will read.
- getPropertiesOrigins(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Gets the origins map from the servlet context.
- getPropertiesStartingWith(String, Properties) - Static method in class org.intermine.util.PropertiesUtil
-
Returns all Properties in props that begin with str
- getPropertiesStartingWith(String) - Static method in class org.intermine.util.PropertiesUtil
-
Returns all global Properties that begin with str
- getProperty(String, String) - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
-
Get a configured property for which an accessor does not exist.
- getProperty() - Method in class org.intermine.web.logic.query.DisplayConstraint.DisplayConstraintOption
-
Get the constraint index to be put in form when this op is selected.
- getProperty(String) - Method in class org.intermine.webservice.server.WebService
-
Get a configuration property by name.
- getPropertyDescriptors() - Method in class org.intermine.api.beans.ObjectDetailsBeanInfo
-
- getPropertyDescriptors() - Method in class org.intermine.api.beans.PartnerLinkBeanInfo
-
- getPropertyName() - Method in class org.intermine.web.struts.EditPropertiesForm
-
- getPropertyValue() - Method in class org.intermine.web.struts.EditPropertiesForm
-
- getProteinNames() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
if an isoform has two ID tags, then the first one is used and the second one is added
as a synonym
- getProtocolAttributes(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the rows needed for protocols from the attribute table.
- getProtocols(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the rows needed from the protocol table.
- getProvider() - Method in class org.intermine.web.struts.oauth2.DelegatedIdentity
-
- getPublicationReferenceList() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Return a ReferenceList containing the Publication Items ids set by addPublication()
- getPublications(ObjectStore) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
-
Retrieve the publications to be updated
- getPublicId() - Method in class org.intermine.webservice.server.lists.ListsServiceInput
-
Returns id of object.
- getPublicTagNames(ClassDescriptor) - Method in class org.intermine.api.profile.TagManager
-
Get all the tags that all users have access to.
- getPublicTagNames(Taggable) - Method in class org.intermine.api.profile.TagManager
-
Get all the tags that all users have access to.
- getPublicTagNames(String, String) - Method in class org.intermine.api.profile.TagManager
-
Get the tags for an object that are visible to all users.
- getPubRefId(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getPubResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return the interesting rows from the pub table.
- getPubs() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getPValue() - Method in class org.intermine.web.struts.WidgetForm
-
- getPValues() - Method in class org.intermine.web.logic.widget.EnrichmentResults
-
Get the probability of enrichment for each attribute value found in the sample.
- getQcb() - Method in class org.intermine.objectstore.query.QueryCollectionReference
-
Gets the QueryClassBag of this QueryReference.
- getQcObject() - Method in class org.intermine.objectstore.query.QueryCollectionReference
-
Gets the InterMineObject of this QueryReference.
- getQcType() - Method in class org.intermine.objectstore.query.QueryCollectionReference
-
Returns the type of the queryclass of this reference
- getQcType() - Method in class org.intermine.objectstore.query.QueryReference
-
Returns the type of the queryclass of this reference
- getQope() - Method in class org.intermine.objectstore.query.PathExpressionField
-
Returns the QueryObjectPathExpression.
- getQualifiedType() - Method in class org.intermine.api.profile.InterMineBag
-
Get the fully qualified type of this bag
- getQueried(String) - Method in class org.intermine.dataloader.EquivalentObjectHints
-
Returns a Set of values that have been tested for a particular class and fieldname.
- getQueries() - Method in class org.intermine.sql.precompute.BestQueryStorer
-
Gets the set of queries added to this object
- getQuery(Collection<String>, String) - Method in class org.intermine.api.bag.BagQuery
-
Return the Query that was passed to the constructor.
- getQuery() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
-
- getQuery(String) - Method in class org.intermine.api.query.MemoryQueryStore
-
- getQuery(String) - Method in interface org.intermine.api.query.QueryStore
-
- getQuery() - Method in class org.intermine.api.results.ExportResultsIterator
-
- getQuery() - Method in interface org.intermine.objectstore.proxy.LazyCollection
-
Returns the Query used by this LazyCollection
- getQuery() - Method in class org.intermine.objectstore.proxy.ProxyCollection
-
Returns the Query used by this LazyCollection
- getQuery(Collection<? extends InterMineObject>) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
-
Returns the Query that will fetch the data represented by this object, given a Collection
of objects to fetch it for.
- getQuery(Collection<Integer>, boolean) - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
-
Returns the Query that will fetch the data represented by this object, given a Collection
of objects to fetch it for.
- getQuery() - Method in class org.intermine.objectstore.query.Results
-
Get the Query that produced this Results object.
- getQuery() - Method in class org.intermine.objectstore.query.ResultsBatches
-
Get the Query that produced this ResultsBatches object.
- getQuery() - Method in class org.intermine.objectstore.query.SubqueryConstraint
-
Get the query.
- getQuery() - Method in class org.intermine.objectstore.query.SubqueryExistsConstraint
-
Get the query.
- getQuery() - Method in class org.intermine.objectstore.querygen.QueryGenUtil.QueryAndClass
-
Returns the query.
- getQuery() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
-
Returns the Query of this Candidate, converting from a String if necessary.
- getQuery() - Method in class org.intermine.sql.precompute.LimitOffsetQuery
-
Getter for the stripped query.
- getQuery() - Method in class org.intermine.sql.precompute.PrecomputedTable
-
Gets the Query that is materialised in this PrecomputedTable
- getQuery() - Method in class org.intermine.sql.query.SubQuery
-
Returns the query contained in the subquery.
- getQuery() - Method in class org.intermine.web.logic.session.QueryCountQueryMonitor
-
Return the Query that was passed to the constructor.
- getQuery(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Returns the PathQuery on the session.
- getQuery(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Returns the PathQuery on the session.
- getQuery(String, List<String>) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
-
Returns the relevant query.
- getQuery(boolean, List<String>) - Method in class org.intermine.web.logic.widget.TableWidgetLdr
-
- getQuery() - Method in class org.intermine.web.struts.QueryForm
-
- getQuery(HttpServletRequest) - Method in class org.intermine.webservice.server.query.QueryToListService
-
Get the pathquery to use for this request.
- getQuery(PathQuery, Profile) - Method in class org.intermine.webservice.server.query.QueryToListService
-
Get the Objectstore Query to run to generate the list.
- getQuery() - Method in class org.intermine.webservice.server.query.result.PathQueryBuilder
-
Returns parsed PathQuery.
- getQuery() - Method in class org.intermine.webservice.server.query.result.PathQueryBuilderForJSONObj
-
For the purposes of exporting into JSON objects the view must be:
Ordered by length, such that Company.departments.name precedes
Company.departments.employees.name
Be constituted so that every class has an attribute on it, root class
included, and every reference along the way.
- getQuery(HttpServletRequest) - Method in class org.intermine.webservice.server.template.TemplateToListService
-
- getQueryBuilder() - Method in class org.intermine.web.struts.ImportQueriesForm
-
Get the queryBuilder field.
- getQueryBuilder(String) - Method in class org.intermine.webservice.server.query.AbstractQueryService
-
Get a path-query builder.
- getQueryClass() - Method in class org.intermine.objectstore.query.ContainsConstraint
-
Returns the QueryClass of the constraint.
- getQueryClass() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
-
Returns the QueryClass of which the field is a member.
- getQueryClass() - Method in class org.intermine.objectstore.query.QueryForeignKey
-
Gets the QueryClass of which this reference is an member.
- getQueryClass() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
-
Returns the QueryClass of which the field is a member.
- getQueryClass() - Method in interface org.intermine.objectstore.query.QueryPathExpressionWithSelect
-
Returns the QueryClass of which the field is a member.
- getQueryClass() - Method in class org.intermine.objectstore.query.QueryReference
-
Gets the QueryClass of which this reference is an member.
- getQueryClass() - Method in class org.intermine.objectstore.query.SubqueryConstraint
-
Get the QueryClass the query is compare with
- getQueryDesc() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
-
- getQueryEvaluable() - Method in class org.intermine.objectstore.query.SubqueryConstraint
-
Get the QueryEvaluable the query is compared with
- getQueryFields(QueryEvaluable) - Static method in class org.intermine.objectstore.query.ConstraintHelper
-
Descends into QueryExpression and QueryFunction objects to find
all instances of QueryField.
- getQueryForWildcards(Collection<String>, String) - Method in class org.intermine.api.bag.BagQuery
-
Return a Query to fetch bag contents for wildcards.
- getQueryInfo(PathQuery) - Method in class org.intermine.api.query.WebResultsExecutor
-
Retrieve an entry from the infoCache.
- getQueryMap() - Method in class org.intermine.web.struts.ImportQueriesForm
-
Return a Map from query name to Query object.
- getQueryMap(BagManager, Profile) - Method in class org.intermine.web.struts.TemplatesImportForm
-
Return a Map from template name to Template object.
- getQueryName() - Method in class org.intermine.web.struts.SaveQueryForm
-
Get the query name
- getQueryNode() - Method in class org.intermine.objectstore.query.BagConstraint
-
Get the QueryNode.
- getQueryOrderable() - Method in class org.intermine.objectstore.query.OrderDescending
-
Return the encapsulated QueryOrderable.
- getQueryService() - Method in class org.intermine.webservice.client.core.ServiceFactory
-
Return a new QueryService for getting query results from.
- getQueryStore() - Method in class org.intermine.api.InterMineAPI
-
- getQueryString() - Method in class org.intermine.objectstore.query.iql.IqlQuery
-
Get the query String
NOTE: this will be unvalidated
- getQueryString() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
-
Returns the String query of this Candidate, converting from Query if necessary.
- getQueryTime() - Method in class org.intermine.objectstore.intermine.ExtraQueryTime
-
Returns the total amount of time spent in extra queries, in milliseconds.
- getQueryToExecute() - Method in class org.intermine.pathquery.PathQuery
-
Get the PathQuery that should be executed.
- getQueryToExecute() - Method in class org.intermine.template.TemplateQuery
-
Fetch the PathQuery to execute for this template.
- getQueryTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices
-
- getQueryTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices
-
- getQueryWithDefaultView(String, Model, WebConfig, String) - Static method in class org.intermine.web.logic.pathqueryresult.PathQueryResultHelper
-
Used for making a query for a reference or collection.
- getQueryXml() - Method in class org.intermine.webservice.server.query.QueryRequestParser
-
Get query XML from a request.
- getRangeConstraint() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Get the range constraint value.
- getRangeLabel() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
Get the value of rangeLabel
- getRangeOp() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
- getRangeQueryOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Returns the set of operators valid for range constraints.
- getRanges() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
- getRangeSetOp() - Method in class org.intermine.api.query.range.ConstraintOptions
-
- getRank(TemplateManager) - Method in class org.intermine.api.tracker.TemplateTracker
-
Return the rank for each public template.It represents a relationship between the templates
executions; a template with rank 1 has been executed more than a template with rank 2.
- getRank(TemplateManager) - Method in class org.intermine.api.tracker.TrackerDelegate
-
Return the rank associated to the templates
- getRatDiseases(String) - Static method in class org.intermine.dwr.AjaxServices
-
Return list of disease ontology terms associated with list of provided rat genes.
- getRatIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a rat id resolver
- getRatIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a rat id resolver
- getRatIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a rat id resolver
- getRawOutput() - Method in class org.intermine.webservice.server.WebService
-
Get access to the underlying print-writer.
- getReader(Set<Integer>) - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
-
Obtain the pubmed esummary information for the organisms
- getReader(Integer) - Static method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
-
- getReader(Set<Integer>) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
-
Obtain the pubmed esummary information for the publications
- getReader() - Method in class org.intermine.webservice.client.results.ResultSet
-
Get a reader over the data, for reading line-by-line.
- getReader(HttpServletRequest) - Method in class org.intermine.webservice.server.lists.ListUploadService
-
Get the reader for the identifiers uploaded with this request.
- getReason() - Method in exception org.intermine.webservice.client.exceptions.ResultException
-
Get the reason for this error.
- getReference() - Method in class org.intermine.objectstore.query.ContainsConstraint
-
Returns the QueryReference of the constraint.
- getReference(String) - Method in class org.intermine.webservice.client.results.Item
-
Get in Item representing the record referenced by a reference field.
- getReference(String) - Method in class org.intermine.xml.full.Item
-
Get a named reference.
- getReferenceLists() - Method in class org.intermine.webservice.server.lists.ListInput
-
- getReferenceName() - Method in class org.intermine.bio.chado.config.CreateCollectionAction
-
Return the referenceName that was passed to the constructor.
- getReferences() - Method in class org.intermine.objectstore.intermine.DatabaseSchema.Fields
-
Returns the Set of references
- getReferences() - Method in class org.intermine.xml.full.Item
-
Get all the references.
- getRefId() - Method in class org.intermine.xml.full.Reference
-
Get the refId of this field
- getRefIds() - Method in class org.intermine.xml.full.ReferenceList
-
Get the references in this collection.
- getRefsAndCollections() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
- getRefsAndCollections() - Method in class org.intermine.web.logic.results.ReportObject
-
Get all the reference and collection fields and values for this object
- getRelationship() - Method in class org.intermine.bio.ontology.OboRelation
-
- getRelease() - Static method in class org.intermine.web.filters.ReleaseEtagFilter
-
- getRelease() - Method in class org.intermine.webservice.client.core.Service
-
- getReleaseVersion() - Method in class org.intermine.api.mines.LocalMine
-
- getReleaseVersion() - Method in interface org.intermine.api.mines.Mine
-
- getReleaseVersion() - Method in class org.intermine.api.mines.RemoteMine
-
- getRelevantConstraints() - Method in class org.intermine.pathquery.PathQuery
-
- getRelevantConstraints() - Method in class org.intermine.template.TemplateQuery
-
- getRenamedBags() - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
-
Get the mapping from old to new names.
- getRenamedClasses() - Method in class org.intermine.api.profile.ModelUpdate
-
Return a map containing the couple previous class and new class
- getRenamedFields() - Method in class org.intermine.api.profile.ModelUpdate
-
Return a map containing the couple previousClass.previuosField and new field
- getRenamedTemplates() - Method in class org.intermine.web.logic.profile.ProfileMergeIssues
-
Get the names of all the templates that failed.
- getReplacedFieldExprs() - Method in class org.intermine.web.displayer.ReportDisplayer
-
Get a list of field names and paths that should be replaced by this displayer - i.e. this
displayer should be shown instead of other fields.
- getReplacedFieldExprs() - Method in class org.intermine.web.logic.results.ReportObject
-
Get fields and paths that are replaced by custom report displayers and should not be shown
in the report page.
- getReplacedFieldNames() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Get the names of fields this displayer replaces.
- getReplacesFields() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Get the comma separated list of field names that should not be displayed on the report page
when this displayer is used.
- getReportDisplayer(String) - Method in class org.intermine.web.logic.results.ReportObject
-
Give us a displayer by a specific name, called by AjaxServices
- getReportDisplayerByName(String, String) - Method in class org.intermine.web.displayer.DisplayerManager
-
Get a specific ReportDisplayer by its name for a given ReportObject type
- getReportDisplayerConfigs() - Method in class org.intermine.web.logic.config.WebConfig
-
Fetch config for the report page displayers.
- getReportDisplayers() - Method in class org.intermine.web.logic.results.ReportObject
-
Get a map from placement (header, summary or a data category) to custom report displayers for
that placement.
- getReportDisplayersForType(String) - Method in class org.intermine.web.displayer.DisplayerManager
-
Get a map from placement string (a data category or summary) to displayers for the given
type.
- getReportObject(HttpSession, String) - Method in class org.intermine.web.struts.ModifyDetails
-
Get a ReportObject from the session given the object id as a string.
- getReportObjects(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Return the ReportObjects Map from the session or create and return it if it doesn't exist.
- getReportPageTemplatesForAspect(String, Set<String>) - Method in class org.intermine.api.template.TemplateManager
-
Get a list of template queries that should appear on report pages for the given type
under the specified aspect.
- getRequest() - Static method in class org.intermine.objectstore.query.PrefetchManager
-
Returns a request for a thread to service.
- getRequestFileName() - Method in class org.intermine.webservice.server.WebService
-
If the request has a filename parameter then use that
for the fileName, otherwise use the default fileName
- getRequiredParameter(String) - Method in class org.intermine.webservice.server.WebService
-
Get a parameter this service deems to be required.
- getResponseBodyAsStream() - Method in class org.intermine.webservice.client.util.HttpConnection
-
- getResponseBodyAsString() - Method in class org.intermine.webservice.client.util.HttpConnection
-
Return the response body, ensuring that the connection is closed
upon completion.
- getResponseCode() - Method in class org.intermine.webservice.client.util.HttpConnection
-
- getResponseHeader(String) - Method in class org.intermine.webservice.client.util.HttpConnection
-
- getResponseStream() - Method in class org.intermine.webservice.client.util.HttpConnection
-
- getResponseTable(Request) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Performs the actual remote request and fetches the results.
- getResponseType() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
-
- getResponseType() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
-
- getResponseType() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
-
- getResult() - Method in interface org.intermine.api.idresolution.Job
-
- getResult() - Method in class org.intermine.api.idresolution.ResolutionJob
-
- getResult() - Method in class org.intermine.api.idresolution.UpgradeJob
-
- getResultElementRows() - Method in class org.intermine.web.logic.results.InlineResultsTable
-
Main method used from report to resolve a tablefull of ResultElements
- getResultElements(int) - Method in class org.intermine.api.results.WebResults
-
Return a List containing a ResultElement object for each element in the given row.
- getResultElements(int) - Method in interface org.intermine.api.results.WebTable
-
Return a List containing a ResultElement object for each element given in the given row.
- getResultRows(PagedTable, HttpServletRequest) - Method in class org.intermine.web.logic.export.http.HttpExporterBase
-
- getResults() - Method in class org.intermine.api.bag.BagQueryResult.IssueResult
-
- getResults() - Method in interface org.intermine.web.logic.widget.DataSetLdr
-
Get the Results object
- getResults() - Method in class org.intermine.web.logic.widget.EnrichmentWidget
-
- getResults() - Method in class org.intermine.web.logic.widget.GraphWidget
-
- getResults() - Method in class org.intermine.web.logic.widget.GraphWidgetLoader
-
- getResults() - Method in class org.intermine.web.logic.widget.HTMLWidget
-
- getResults() - Method in class org.intermine.web.logic.widget.TableWidget
-
- getResults() - Method in class org.intermine.web.logic.widget.Widget
-
Return the result that represents the data from this widget.
- getResults() - Method in class org.intermine.webservice.client.results.JSONResult
-
- getResults(PathQuery, Page) - Method in class org.intermine.webservice.client.services.QueryService
-
- getResults(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
-
Returns a specific set of the results of the specified PathQuery.
- getResults(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
-
Returns a set of the results for the given template template with the given parameters,
defined by the index of the first result you want back, and the maximum page size.
- getResults(TemplateQuery, Page) - Method in class org.intermine.webservice.client.services.TemplateService
-
- getResults() - Method in class org.intermine.webservice.server.output.MemoryOutput
-
Returns results added to output
- getResultsAsList() - Method in class org.intermine.web.logic.results.InlineResultsTable
-
- getResultsBatches() - Method in class org.intermine.objectstore.query.Results
-
Returns the underlying ResultsBatches object that this object is using, in order to create
more Results objects (with different settings) from it.
- getResultsCount() - Method in class org.intermine.webservice.server.output.MemoryOutput
-
}
- getResultsCount() - Method in class org.intermine.webservice.server.output.Output
-
- getResultsCount() - Method in class org.intermine.webservice.server.output.StreamedOutput
- getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONDataTableRowResultProcessor
-
- getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONObjResultProcessor
-
- getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONResultProcessor
-
The method a processor must implement to produce a results iterator.
- getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONRowResultProcessor
-
- getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONSummaryProcessor
-
- getResultsIterator(Iterator<List<ResultElement>>) - Method in class org.intermine.webservice.server.output.JSONTableResultProcessor
-
- getResultsKey() - Method in class org.intermine.webservice.server.branding.BrandingService
-
- getResultsKey() - Method in class org.intermine.webservice.server.core.JSONService
-
- getResultsKey() - Method in class org.intermine.webservice.server.data.DataService
-
- getResultsKey() - Method in class org.intermine.webservice.server.idresolution.IdResolutionService
-
- getResultsKey() - Method in class org.intermine.webservice.server.idresolution.JobResultsService
-
- getResultsKey() - Method in class org.intermine.webservice.server.idresolution.JobStatusService
-
- getResultsKey() - Method in class org.intermine.webservice.server.lists.ListShareCreationService
- getResultsKey() - Method in class org.intermine.webservice.server.lists.ListShareDetailsService
-
- getResultsKey() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationAcceptanceService
-
- getResultsKey() - Method in class org.intermine.webservice.server.lists.ListSharingInvitationService
-
- getResultsKey() - Method in class org.intermine.webservice.server.query.QueryStoreService
-
- getResultsKey() - Method in class org.intermine.webservice.server.query.SavedQueryRetrievalService
-
- getResultsKey() - Method in class org.intermine.webservice.server.SchemaListService
-
- getResultsKey() - Method in class org.intermine.webservice.server.SessionService
-
- getResultsKey() - Method in class org.intermine.webservice.server.SummaryService
-
- getResultsKey() - Method in class org.intermine.webservice.server.template.SingleTemplateService
-
- getResultsKey() - Method in class org.intermine.webservice.server.user.NewDeletionTokenService
-
- getResultsKey() - Method in class org.intermine.webservice.server.user.PermaTokenInfoService
-
- getResultsKey() - Method in class org.intermine.webservice.server.user.ReadPreferencesService
-
- getResultsKey() - Method in class org.intermine.webservice.server.user.TokenService
-
- getResultsKey() - Method in class org.intermine.webservice.server.user.TokensService
-
- getResultsKey() - Method in class org.intermine.webservice.server.user.WhoAmIService
-
- getResultsKey() - Method in class org.intermine.webservice.server.VersionService
-
- getResultsSize(String) - Static method in class org.intermine.dwr.AjaxServices
-
Return the number of rows of results from the query with the given query id.
- getResultsTable(HttpSession, String) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Given a table identifier, return the cached PagedTable.
- getResultsTablesLib() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
-
- getResultsWithoutInit() - Method in class org.intermine.objectstore.query.ClobAccess
-
Returns the (possibly uninitialised) results object used internally by this object, for use
by subclass constructors.
- getResultTable() - Method in interface org.intermine.web.logic.widget.DataSetLdr
-
Return the result table that represents the data from this widget.
- getResultTable() - Method in class org.intermine.web.logic.widget.GraphWidgetLoader
-
- getReturnToString() - Method in class org.intermine.web.struts.LoginForm
-
Return the returnToString set by setReturnToURL().
- getReverseAliases() - Method in class org.intermine.objectstore.query.Query
-
Returns the map of String aliases to QuerySelectables and FromElements
- getRight() - Method in class org.intermine.objectstore.query.OverlapConstraint
-
Returns the right OverlapRange.
- getRight() - Method in class org.intermine.sql.query.Constraint
-
Returns the right argument of the constraint.
- getRight() - Method in class org.intermine.sql.query.InListConstraint
-
Returns the right Set of Constants.
- getRight() - Method in class org.intermine.sql.writebatch.Row
-
Returns right.
- getRightArgument(Constraint) - Static method in class org.intermine.objectstore.query.ConstraintHelper
-
Get the right argument of the given constraint, will return null
if passed a ConstraintSet or a MultipleInBagConstraint.
- getRightColName() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
-
Returns the right column name.
- getRightField() - Method in class org.intermine.api.query.range.ConstraintOptions
-
Defaults to "end".
- getRightOp() - Method in class org.intermine.api.query.range.ConstraintOptions
-
- getRootClass() - Method in class org.intermine.pathquery.PathQuery
-
Returns the root path for this query, if the query verifies correctly.
- getRootCVTerms() - Method in class org.intermine.bio.chado.ChadoCV
-
Return a Set of the root CVTerms in this CV - ie. those with no parents.
- getRootElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
-
- getRootElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
-
- getRootElement() - Method in class org.intermine.webservice.server.user.UserDataFormatter
-
- getRootNode() - Method in class org.intermine.pathquery.LogicExpression
-
Get the root node.
- getRootUrl() - Method in class org.intermine.webservice.client.core.Service
-
Returns service's root URL.
- getRowElement() - Method in class org.intermine.webservice.server.output.HTMLTableFormatter
-
- getRowElement() - Method in class org.intermine.webservice.server.output.XMLFormatter
-
- getRowElement() - Method in class org.intermine.webservice.server.user.UserDataFormatter
-
- getRowFormatter() - Method in class org.intermine.webservice.server.output.FlatFileFormatter
-
Get the row formatter
- getRowIterator(PathQuery, Page) - Method in class org.intermine.webservice.client.services.QueryService
-
- getRowIterator(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
-
Returns a specific set of the results of a specified PathQuery as an iterator.
- getRowIterator(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
-
Returns an iterator over a subset of rows for the template
when run with the given parameters.
- getRowIterator(TemplateQuery, Page) - Method in class org.intermine.webservice.client.services.TemplateService
-
- getRowListIterator(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Get an iterator over the results of a query.
- getRowListIterator(T, Page) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Get an iterator over the results of a query.
- getRowListIterator(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
-
Get an iterator over the results of a query.
- getRowListIterator(String) - Method in class org.intermine.webservice.client.services.QueryService
-
Get an iterator over the results of a query.
- getRowListIterator(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
-
Get an iterator over the results of a query.
- getRowListIterator(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
-
Get an iterator over the results of a query.
- getRowMapIterator(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Get an iterator over the results of a query.
- getRowMapIterator(T, Page) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Get an iterator over the results of a query.
- getRowMapIterator(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
-
Get an iterator over the results of a query.
- getRowMapIterator(String) - Method in class org.intermine.webservice.client.services.QueryService
-
Get an iterator over the results of a query.
- getRowMapIterator(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
-
Get an iterator over the results of a query.
- getRowMapIterator(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
-
Get an iterator over the results of a query.
- getRows(PathQuery) - Method in class org.intermine.api.mines.LocalMine
-
- getRows(String) - Method in class org.intermine.api.mines.LocalMine
-
- getRows(PathQuery) - Method in interface org.intermine.api.mines.Mine
-
Run a path query and get back all the results.
- getRows(String) - Method in interface org.intermine.api.mines.Mine
-
Run a path query and get back all the results.
- getRows(PathQuery) - Method in class org.intermine.api.mines.RemoteMine
-
- getRows(String) - Method in class org.intermine.api.mines.RemoteMine
-
- getRows() - Method in class org.intermine.objectstore.query.ResultsInfo
-
Returns the estimated number of rows in the results.
- getRows() - Method in class org.intermine.sql.query.ExplainResult
-
Returns the number of rows estimated by the database for this query.
- getRows() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Return the currently visible rows of the table as a List of Lists of ResultElement objects.
- getRows() - Method in class org.intermine.web.tags.table.TableTag
-
- getRows(Request, List<String>) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Performs the actual remote request and fetches the results.
- getRows(PathQuery, Page) - Method in class org.intermine.webservice.client.services.QueryService
-
- getRows(TemplateQuery, Page) - Method in class org.intermine.webservice.client.services.TemplateService
-
- getRows() - Method in class org.intermine.webservice.server.core.SubTable
-
- getRowsAsLists() - Method in class org.intermine.webservice.client.results.RowResultSet
-
Get the data for this result set in a parsed form.
- getRowsAsLists(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Get results for a query as rows of objects.
- getRowsAsLists(T, Page) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Get results for a query as rows of objects.
- getRowsAsLists(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
-
Get results for a query as rows of objects.
- getRowsAsLists(String) - Method in class org.intermine.webservice.client.services.QueryService
-
Get results for a query as rows of objects.
- getRowsAsLists(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
-
Get results for a query as rows of objects.
- getRowsAsLists(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
-
Get results for a query as rows of objects.
- getRowsAsMaps() - Method in class org.intermine.webservice.client.results.RowResultSet
-
Get the data for this result set in a parsed form.
- getRowsAsMaps(T) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Get results for a query as rows of objects.
- getRowsAsMaps(T, Page) - Method in class org.intermine.webservice.client.services.AbstractQueryService
-
Get results for a query as rows of objects.
- getRowsAsMaps(String, Page) - Method in class org.intermine.webservice.client.services.QueryService
-
Get results for a query as rows of objects.
- getRowsAsMaps(String) - Method in class org.intermine.webservice.client.services.QueryService
-
Get results for a query as rows of objects.
- getRowsAsMaps(String, List<TemplateParameter>, Page) - Method in class org.intermine.webservice.client.services.TemplateService
-
Get results for a query as rows of objects.
- getRowsAsMaps(String, List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService
-
Get results for a query as rows of objects.
- getRowsFromBatch(int, int, int, boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
-
Gets a range of rows from within a batch
- getRowspan() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
-
Returns the rowspan.
- getRowSpan() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
-
Used from JSP in rowspan attr of
- getRowsToDelete() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
-
Returns the Set of rows to delete.
- getRowsToInsert() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
-
Returns the Set of rows to insert.
- getRunningQueryController(String, HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Get the QueryMonitor object corresponding to a running query id (qid).
- getSampleQuery(boolean) - Method in class org.intermine.web.logic.widget.EnrichmentWidgetImplLdr
-
- getSampleSize() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
-
The sample size, n.
- getSampleSize() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
-
- getSavedBag(String, String) - Method in class org.intermine.api.bag.SharedBagManager
-
Perform a query to retrieve a bag's backing SavedBag
- getSavedBagId() - Method in class org.intermine.api.profile.StorableBag
-
- getSavedBags() - Method in class org.intermine.api.profile.Profile
-
Get the value of savedBags
- getSavedBagsByStatus() - Method in class org.intermine.api.profile.Profile
-
Get the saved bags in a map of "status key" => map of lists
- getSavedBagStatus() - Method in class org.intermine.dwr.AjaxServices
-
This method gets the latest bags from the session (SessionMethods) and returns them in JSON
- getSavedQueries() - Method in class org.intermine.api.profile.Profile
-
Get the value of savedQueries
- getSavedTemplateQuery() - Method in class org.intermine.api.template.ApiTemplate
-
Gets the saved template query object.
- getSavedTemplates() - Method in class org.intermine.api.profile.Profile
-
Get the users saved templates
- getSchema() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Returns the DatabaseSchema used by this ObjectStore.
- getSchemaLocation(HttpServletRequest) - Static method in class org.intermine.webservice.server.query.AbstractQueryService
-
- getScope() - Method in class org.intermine.web.struts.TemplateForm
-
Get the template scope.
- getScore() - Method in class org.intermine.api.lucene.KeywordSearchHit
-
score
- getScore() - Method in class org.intermine.bio.io.bed.BEDRecord
-
- getScore() - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- getScore() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the score field of this record.
- getScore() - Method in class org.intermine.web.search.KeywordSearchResult
-
return score
- getSearchHits(BrowseHit[], Map<Integer, InterMineObject>) - Static method in class org.intermine.api.lucene.KeywordSearch
-
- getSearchIndex(String) - Method in class org.intermine.api.search.SearchRepository
-
Retrieve a search index for a given type of web searchable objects.
- getSearchItems() - Method in class org.intermine.api.search.SearchRepository
-
Returns an unmodifiable view of the the search items observed by this
repository.
- getSearchRepository() - Method in class org.intermine.api.profile.Profile
-
Get the SearchRepository for this Profile.
- getSearchTracksDataTable(String) - Method in class org.intermine.dwr.TrackAjaxServices
-
- getSearchTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices
-
- getSecondFieldName() - Method in class org.intermine.objectstore.query.QueryField
-
Returns the name of the second field.
- getSecondLastClassDescriptor() - Method in class org.intermine.pathquery.Path
-
Returns the second to last ClassDescriptor in the path.
- getSection(Collection<String>) - Method in class org.intermine.pathquery.LogicExpression
-
Take a Collection of String variable names, and return the part of the Logic Expression that
contains those variables.
- getSectionTitle() - Method in class org.intermine.web.logic.config.FieldConfig
-
Get the section title (if sectionOnRight == true).
- getSegmentedFeatures() - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return a list of types where one logical feature is represented as multiple rows in the
feature table.
- getSelect() - Method in class org.intermine.objectstore.query.Query
-
Gets the SELECT list
- getSelect() - Method in interface org.intermine.objectstore.query.Queryable
-
Returns the SELECT list.
- getSelect() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
-
Returns the SELECT list.
- getSelect() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
-
Returns the SELECT list.
- getSelect() - Method in class org.intermine.sql.query.Query
-
Gets the list of select fields for this query.
- getSelected() - Method in class org.intermine.web.struts.ModifyTemplateForm
-
Gets the selected templates
- getSelected() - Method in class org.intermine.web.struts.WidgetForm
-
- getSelectedAsString() - Method in class org.intermine.web.struts.WidgetForm
-
returns the value of the checkboxes checked by the user on the form.
- getSelectedBags() - Method in class org.intermine.web.struts.ModifyBagForm
-
Gets the selected bags
- getSelectedClass() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
- getSelectedColumn() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
- getSelectedConstraint() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Returns the constraint type selected.
- getSelectedElements() - Method in class org.intermine.web.struts.ModifyBagDetailsForm
-
Get a String array of selected bag elements
- getSelectedExtraAttribute() - Method in class org.intermine.web.struts.WidgetForm
-
- getSelectedExtraValue() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
If editing an existing LOOKUP constraint return the value selected for the extra constraint
field.
- getSelectedObjects() - Method in class org.intermine.web.struts.BagUploadConfirmForm
-
Gets the ids of the selected objects
- getSelectedObjects() - Method in class org.intermine.web.struts.SaveBagForm
-
Gets the selected objects
- getSelectedOp() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
If the bag is selected, return the value setted with the method setSelectedBagOp
If editing an existing constraint return the operation used.
- getSelectedQueries() - Method in class org.intermine.web.struts.ModifyQueryForm
-
Gets the selected queries
- getSelectedValue() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
If editing an existing constraint, return the selected value.
- getSelectionIds() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
- getSeqClsName() - Method in class org.intermine.bio.dataconversion.GFF3Converter
-
Return the sequence class name that was passed to the constructor.
- getSeqIdentifier(String) - Method in class org.intermine.bio.dataconversion.GFF3SeqHandler
-
Return the identifier of this sequence, default implementation returns the id passed to it.
- getSequence() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Return the sequence Item set by setSequence()
- getSequence() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getSequence(Set<Object>) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Return the sequence number representing the state of the ObjectStore.
- getSequence(Set<Object>) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Returns an object representing the current state of the database, for fail-fast concurrency
control.
- getSequence(Set<Object>) - Method in interface org.intermine.objectstore.ObjectStore
-
Return the sequence number representing the state of the ObjectStore.
- getSequence(Set<Object>) - Method in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
Returns an object representing the current state of the database, for fail-fast concurrency
control.
- getSequence(Set<Object>) - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Return the sequence number representing the state of the ObjectStore.
- getSequence() - Method in class org.intermine.objectstore.query.Results
-
Returns the sequence that this Results object was created with
- getSequence() - Method in class org.intermine.objectstore.query.ResultsBatches
-
Returns the sequence that this ResultsBatches object was created with
- getSequenceID() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the sequenceID field of this record.
- getSequenceOntology() - Static method in class org.intermine.bio.ontology.SequenceOntologyFactory
-
- getSequenceOntology(File, File) - Static method in class org.intermine.bio.ontology.SequenceOntologyFactory
-
Given an OBO file, create a Sequence Ontology object
- getSequenceOntologyRefId() - Method in class org.intermine.bio.dataconversion.BioDBConverter
-
- getSequenceOntologyRefId() - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
-
- getSequenceOntologyRefId() - Method in class org.intermine.bio.dataconversion.BioFileConverter
-
- getSerial() - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Gets an ID number which is unique in the database.
- getSerial() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Gets an ID number which is unique in the database.
- getSerial() - Method in interface org.intermine.objectstore.ObjectStore
-
Gets an ID number which is unique in the database.
- getSerial() - Method in class org.intermine.objectstore.ObjectStorePassthruImpl
-
Gets an ID number which is unique in the database.
- getSerial() - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
-
Gets an ID number which is unique in the database.
- getSerialWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Gets an ID number which is unique in the database, given a Connection.
- getSerialWithConnection(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Overrides, in order to store recentSequences.
- getSeriesLabels() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- getSeriesPath() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- getSeriesValues() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- getService(String, String) - Method in class org.intermine.webservice.client.core.ServiceFactory
-
Creates a new service for general use.
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.core.ConfigurableWebServiceServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.core.RestfulServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.core.WebServiceServlet
-
Implement this to route requests.
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.idresolution.IdResolutionServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.AvailableListsServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListRenameServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListShareServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.lists.ListSharingInvitationServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.query.QueryUploadServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.search.QuickSearchServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.template.result.TemplateResultServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.template.TemplateToListServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.template.TemplateUploadServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.DeregistrationTokenServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.NewUserServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.PermaTokensServlet
-
- getService(WebServiceServlet.Method) - Method in class org.intermine.webservice.server.user.WhoAmIServlet
-
- getServiceBaseURL() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
-
- getServices() - Method in class org.intermine.webservice.server.ServiceListingHandler
-
- getServiceUrl() - Method in interface org.intermine.webservice.client.core.Request
-
Returns service URL.
- getServiceUrl() - Method in class org.intermine.webservice.client.core.RequestImpl
-
Returns service URL.
- getSession() - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
Get the session
- getSession() - Method in class org.intermine.webservice.server.core.SessionlessRequest
-
- getSession(boolean) - Method in class org.intermine.webservice.server.core.SessionlessRequest
-
- getSessionIdentifier() - Method in class org.intermine.api.tracker.track.TrackAbstract
-
Return the session id
- getSharedBags(Profile) - Method in class org.intermine.api.bag.BagManager
-
Fetch the shared bags for the given profile.
- getSharedBags(Profile) - Method in class org.intermine.api.bag.SharedBagManager
-
Return a map containing the bags that the user in input has access because shared by
someone else
- getSharedBags() - Method in class org.intermine.api.profile.Profile
-
Return the shared bags for the profile.
- getSharedBagsContainingId(Profile, Integer) - Method in class org.intermine.api.bag.BagManager
-
Fetch bags shared by another user that contain the given id.
- getShortName() - Method in class org.intermine.bio.util.OrganismData
-
Get the short of this organism, eg.
- getShowIdentifier() - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
-
Used from JSP
- getShowImmediately() - Method in class org.intermine.web.displayer.ReportDisplayer
-
- getShowImmediately() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Should we display this 'splayer immediately, wo/ waiting for the AJAX call?
- getShowInHeader() - Method in class org.intermine.web.logic.config.InlineListConfig
-
- getShowInInlineCollection() - Method in class org.intermine.web.logic.config.FieldConfig
-
Return the value of the showInInlineCollection flag
- getShowInListAnalysisPreviewTable() - Method in class org.intermine.web.logic.config.FieldConfig
-
- getShowInQB() - Method in class org.intermine.web.logic.config.FieldConfig
-
- getShowInResults() - Method in class org.intermine.web.logic.config.FieldConfig
-
Return the value of the showInResults flag
- getShowInSummary() - Method in class org.intermine.web.logic.config.FieldConfig
-
Return the value of the showInSummary flag
- getShowLinksToObjects() - Method in class org.intermine.web.logic.config.InlineListConfig
-
- getShowLinksToObjects() - Method in class org.intermine.web.logic.results.InlineList
-
- getShowOnLeft() - Method in class org.intermine.web.logic.config.Displayer
-
- getSimpleClass(Class<? extends FastPathObject>) - Static method in class org.intermine.util.DynamicUtil
-
Returns the result of decomposeClass if that is a single class, or throws an exception if
there are more than one.
- getSimpleClass(FastPathObject) - Static method in class org.intermine.util.DynamicUtil
-
For the given object returns the result of decomposeClass if that is a single class, or
throws an exception if there are more than one class.
- getSimpleClassName(Class<?>) - Static method in class org.intermine.util.DynamicUtil
-
Returns the simple class name for the given class or throws an exception if
there are more than one.
- getSimpleClassName(FastPathObject) - Static method in class org.intermine.util.DynamicUtil
-
Returns the simple class name for the given object or throws an exception if
there are more than one.
- getSimplePathQuery() - Method in class org.intermine.web.logic.widget.GraphWidget
-
Returns the pathquery based on the classkey.
- getSingleUseKey() - Method in class org.intermine.api.profile.Profile
-
Return a single use API key for this profile
- getSingleUseKey() - Static method in class org.intermine.dwr.AjaxServices
-
Return the single use API key for the current profile
- getSize() - Method in class org.intermine.api.profile.InterMineBag
-
- getSize() - Method in class org.intermine.api.profile.InvalidBag
-
- getSize() - Method in class org.intermine.api.profile.StorableBag
-
Returns the size of the bag.
- getSize() - Method in class org.intermine.sql.writebatch.IndirectionTableBatch
-
Returns the current amount of data, in bytes, held in this object.
- getSize() - Method in interface org.intermine.sql.writebatch.Table
-
Returns the current amount of data, in bytes, held in this object.
- getSize() - Method in class org.intermine.sql.writebatch.TableBatch
-
Returns the current amount of data, in bytes, held in this object.
- getSize() - Method in class org.intermine.web.logic.results.DisplayField
-
Get the size of this collection
- getSize() - Method in class org.intermine.web.logic.results.InlineList
-
- getSize() - Method in class org.intermine.web.logic.widget.PopulationInfo
-
- getSize() - Method in class org.intermine.webservice.client.lists.ItemList
-
- getSize() - Method in class org.intermine.webservice.client.results.Page
-
Get the maximum size of this page.
- getSize() - Method in class org.intermine.webservice.server.core.Page
-
- getSizeFields() - Method in class org.intermine.web.autocompletion.LuceneObjectClass
-
getSizeFields
- getSizeValues() - Method in class org.intermine.web.autocompletion.LuceneObjectClass
-
getSizeValues
- getSizeValuesForField(String) - Method in class org.intermine.web.autocompletion.LuceneObjectClass
-
getSizeValuesForField
- getSkeleton() - Method in class org.intermine.dataloader.Source
-
Getter for skeleton.
- getSkeletonSource(String, String) - Method in interface org.intermine.dataloader.IntegrationWriter
-
Converts a string describing the data source into a Source object suitable for passing to the
store method as the skeleton source.
- getSkeletonSource(String, String) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
-
Converts a string describing the data source into a Source object suitable for passing to the
store method as the skeleton source.
- getSome(String...) - Method in class org.intermine.web.security.KeyStorePublicKeySource
-
- getSome(String...) - Method in interface org.intermine.web.security.PublicKeySource
-
Get multiple keys given a set of names.
- getSoTerm(DataConverter, Item, String, String) - Static method in class org.intermine.bio.dataconversion.BioStoreHook
-
Get and store a SO term based on intermine item's class or featureType (if provided).
- getSource() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the source field of this record.
- getSource(Integer, String) - Method in class org.intermine.dataloader.DataTracker
-
Retrieve the Source for a specified field of an Object stored in the database.
- getSource(String) - Method in class org.intermine.dataloader.ObjectDescription
-
Gets the source associated with the given fieldname.
- getSourcePrimaryKeys(Source, Model) - Static method in class org.intermine.dataloader.DataLoaderHelper
-
Fetch all primary keys for the given source.
- getSpecies() - Method in class org.intermine.bio.util.OrganismData
-
Get the species of this organism.
- getSQLString() - Method in class org.intermine.sql.precompute.PrecomputedTable
-
Get a "CREATE TABLE" SQL statement for this PrecomputedTable.
- getSQLString() - Method in class org.intermine.sql.query.AbstractConstraint
-
Returns a String representation of this AbstractConstraint object, suitable for forming
part of an SQL query.
- getSQLString() - Method in class org.intermine.sql.query.AbstractTable
-
Returns a String representation of this AbstractTable object, suitable for forming
part of an SQL query.
- getSQLString() - Method in class org.intermine.sql.query.AbstractValue
-
Returns a String representation of this AbstractValue object, suitable for forming
part of an SQL query.
- getSQLString() - Method in class org.intermine.sql.query.Constant
-
Returns a String representation of this Constant object, suitable for forming part of an
SQL query.
- getSQLString() - Method in class org.intermine.sql.query.Constraint
-
Returns a String representation of this Constraint object, suitable for forming part of an
SQL query.
- getSQLString() - Method in class org.intermine.sql.query.ConstraintSet
-
Returns a String representation of this ConstraintSet object, suitable for forming part of
an SQL query.
- getSQLString() - Method in class org.intermine.sql.query.Field
-
Returns a String representation of this Field object, suitable for forming part of an SQL
query.
- getSQLString() - Method in class org.intermine.sql.query.Function
-
Returns a String representation of this Function object, suitable for forming part of an
SQL query.
- getSQLString() - Method in class org.intermine.sql.query.InListConstraint
-
Returns a String representation of this InListConstraint object, suitable for forming part
of an SQL Query.
- getSQLString() - Method in class org.intermine.sql.query.NotConstraint
-
Returns a String representation of this Constraint object, suitable for forming part of an
SQL query.
- getSQLString() - Method in class org.intermine.sql.query.OrderDescending
-
Returns a String representation of this AbstractValue object, suitable for forming
part of an SQL query.
- getSQLString() - Method in class org.intermine.sql.query.Query
-
Convert this Query into a SQL String query.
- getSQLString() - Method in class org.intermine.sql.query.SelectValue
-
Returns a String representation of this Field object, suitable for forming part of an SQL
SELECT list.
- getSQLString() - Method in interface org.intermine.sql.query.SQLStringable
-
Returns a String representation of this object, suitable for forming part of an SQL query.
- getSQLString() - Method in class org.intermine.sql.query.SubQuery
-
Returns a String representation of this SubQuery object, auitable for forming part of an SQL
query.
- getSQLString() - Method in class org.intermine.sql.query.SubQueryConstraint
-
Returns a String representation of this SubQueryConstraint object, suitable for forming part
of an SQL Query.
- getSQLString() - Method in class org.intermine.sql.query.Table
-
Returns a String representation of this Table object, suitable for forming part of an SQL
query.
- getSQLStringForPrecomputedTable(String) - Method in class org.intermine.sql.query.Query
-
Convert this Query into a SQL String query, without regard to the other members of the the
UNION, with an extra field in the SELECT list.
- getSQLStringNoUnion() - Method in class org.intermine.sql.query.Query
-
Convert this Query into a SQL String query, without regard to the other members of the
UNION.
- getSrc() - Method in class org.intermine.web.logic.config.Displayer
-
Get the source of this displayer
- getStandardDeviation() - Method in class org.intermine.webservice.client.services.QueryService.NumericSummary
-
- getStandardIndexStatements(ClassDescriptor, Map<String, IndexStatement>) - Method in class org.intermine.task.CreateIndexesTask
-
Add indexes for primary keys, indirection tables and 1-N relations to the relevant tables for
a given ClassDescriptor
- getStar(Model, String) - Static method in class org.intermine.webservice.client.util.PQUtil
-
Get a list of all the path-strings for the attributes of a given class.
- getStart() - Method in interface org.intermine.api.query.range.Range
-
- getStart() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the start field of this record.
- getStart() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
-
Get start value
- getStart() - Method in class org.intermine.objectstore.query.OverlapRange
-
Returns the left parameter.
- getStart() - Method in class org.intermine.objectstore.query.ResultsInfo
-
Returns the estimated amount of time taken to produce the first row of the results.
- getStart() - Method in class org.intermine.sql.query.ExplainResult
-
Returns the number of page requests before the first row is returned, estimated by the
database for this query.
- getStart() - Method in class org.intermine.webservice.client.results.Page
-
Get the start index of this page.
- getStart() - Method in class org.intermine.webservice.server.core.Page
-
Get the index of the first row that is requested.
- getStart() - Method in class org.intermine.webservice.server.WebServiceInput
-
Returns index of first returned result
- getStartClass() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- getStartClassDescriptor() - Method in class org.intermine.pathquery.Path
-
Return the ClassDescriptor of the first element in the path.
- getStartClassDisplay() - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- getStartedAt() - Method in interface org.intermine.api.idresolution.Job
-
- getStartedAt() - Method in class org.intermine.api.idresolution.ResolutionJob
-
- getStartedAt() - Method in class org.intermine.api.idresolution.UpgradeJob
-
- getStartingPoints() - Method in class org.intermine.web.logic.aspects.Aspect
-
Get a List of starting point class names.
- getStartRow() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Get the index of the first row of this page
- getState() - Method in class org.intermine.api.profile.InterMineBag
-
Return the bag state: current, not current, to upgrade
- getState() - Method in class org.intermine.api.profile.InvalidBag
-
- getState() - Method in class org.intermine.api.profile.StorableBag
-
Return a string representing the state of this bag (eg.
- getState(String) - Method in class org.intermine.web.logic.results.WebState
-
- getStatementCreatingTable() - Method in class org.intermine.api.tracker.AbstractTracker
-
Generate the sql statement to create the table used by the tracker
- getStatementCreatingTable() - Method in class org.intermine.api.tracker.KeySearchTracker
-
- getStatementCreatingTable() - Method in class org.intermine.api.tracker.ListTracker
-
Generate the sql statement to create the table used by the tracker
- getStatementCreatingTable() - Method in class org.intermine.api.tracker.LoginTracker
-
Generate the sql statement to create the table used by the tracker
- getStatementCreatingTable() - Method in class org.intermine.api.tracker.QueryTracker
-
Generate the sql statement to create the table used by the tracker
- getStatementCreatingTable() - Method in class org.intermine.api.tracker.TemplateTracker
-
Generate the sql statement to create the table used by the tracker
- getStates() - Method in class org.intermine.web.logic.results.WebState
-
- getStaticPage(String, String) - Static method in class org.intermine.web.logic.WebUtil
-
Return the contents of the page given by prefixURLString + '/' + path as
a String.
- getStatus() - Method in interface org.intermine.api.idresolution.Job
-
- getStatus() - Method in class org.intermine.api.idresolution.ResolutionJob
-
- getStatus() - Method in class org.intermine.api.idresolution.UpgradeJob
-
- getStatus() - Method in class org.intermine.objectstore.query.ResultsInfo
-
Returns an integer describing the type of estimate getRows() returns.
- getStatus() - Method in class org.intermine.webservice.client.lists.ItemList
-
Any status other than CURRENT
indicated this list needs manual attention in the
webapp.
- getStocksResultSet(Connection) - Method in class org.intermine.bio.dataconversion.StockProcessor
-
Return the interesting rows from the features table.
- getStrain(Set<String>) - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
Get strain taxons.
- getStrain() - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
-
- getStrain(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig
-
- getStrain(String) - Method in class org.intermine.bio.util.OrganismRepository
-
Get strains for given taxon ID
- getStrains() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
used for testing
- getStrand() - Method in class org.intermine.bio.io.bed.BEDRecord
-
- getStrand() - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- getStrand() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the strand field of this record.
- getStrand() - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
-
Get strand value
- getString(String) - Static method in class org.intermine.api.query.codegen.JSStrings
-
- getString(String, Object...) - Static method in class org.intermine.api.query.codegen.JSStrings
-
- getString(String) - Method in class org.intermine.webservice.client.results.Item
-
Get a property known to be a string.
- getStringResponse(Request, Integer) - Method in class org.intermine.webservice.client.core.Service
-
Performs the request and returns the result as a string.
- getStringResponse(Request) - Method in class org.intermine.webservice.client.core.Service
-
Performs the request and returns the result as a string.
- getStructure() - Method in class org.intermine.web.logic.query.MetadataNode
-
Returns the structure of the tree.
- getStructure() - Method in class org.intermine.web.logic.TreeNode
-
Returns the structure of the tree.
- getStyle() - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
-
Returns element style.
- getStyleClass() - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
-
Returns css style class of element.
- getSubclass() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
-
Returns the subclass if it exists.
- getSubclass() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
-
Returns the subclass if it exists.
- getSubclass() - Method in class org.intermine.web.logic.querybuilder.SummaryPath
-
Returns the name of the subclass on this path, if there is one.
- getSubClassConstraintPaths() - Method in class org.intermine.pathquery.Path
-
Returns a Map from simplified path string (with dots instead of colons, and no constraints)
to constraint class name.
- getSubclasses() - Method in class org.intermine.pathquery.PathQuery
-
Returns the subclass Map for this query, if the query verifies correctly.
- getSubclassValue() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Gets the value of subclassValue
- getSubject() - Method in class org.intermine.web.struts.ContactForm
-
- getSubmissionOrganism(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the row needed for the organism.
- getSubmissions(Connection) - Method in class org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor
-
Return the rows needed for the submission table.
- getSubSequence() - Method in class org.intermine.objectstore.query.ClobAccess
-
Returns true if this object is a subsequence of a main Clob.
- getSubtab(String) - Method in class org.intermine.web.logic.results.WebState
-
- getSubtabs() - Method in class org.intermine.web.logic.results.WebState
-
map of tab --> subtab
- getSubTitle() - Method in class org.intermine.web.logic.aspects.Aspect
-
Get the subtitle
- getSubTitles() - Method in class org.intermine.web.logic.config.Type
-
- getSubtractLists() - Method in class org.intermine.webservice.server.lists.ListInput
-
- getSubType() - Method in class org.intermine.webservice.client.core.ContentType
-
- getSuffix() - Method in class org.intermine.web.logic.config.HeaderConfigTitle.TitlePart
-
A suffix that may be an HTML tag to appear after this part in the title.
- getSummary(Source) - Method in class org.intermine.dataloader.BaseEquivalentObjectFetcher
-
Returns a StringBuffer containing summary information.
- getSummary(Source) - Method in class org.intermine.dataloader.HintingFetcher
-
Returns a StringBuffer containing summary information.
- getSummary(PathQuery, String) - Method in class org.intermine.webservice.client.services.QueryService
-
Get a summary for the values in column of a query.
- getSummary(PathQuery, String, Page) - Method in class org.intermine.webservice.client.services.QueryService
-
Get a summary for the values in column of a query.
- getSuperuser() - Method in class org.intermine.api.profile.Profile
-
Alias of isSuperUser() for jsp purposes.
- getSuperuser() - Method in class org.intermine.api.profile.ProfileManager
-
Return the super user name set in the properties file
- getSuperuserProfile() - Method in class org.intermine.api.profile.ProfileManager
-
Return the superuser profile set in the properties file
- getSuperuserProfile(Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
-
Return the super user
- getSuperUsers() - Method in class org.intermine.api.profile.ProfileManager
-
Return a list of users with 'superuser' role
- getSuperUsers() - Method in class org.intermine.web.struts.ModifySuperUserForm
-
Get the super users
- getSuperUsersProfile() - Method in class org.intermine.api.profile.ProfileManager
-
Return a list of profile with 'superuser' role
- getSwitchable() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Return the value on, off, locked depending on the constraint SwitchOffAbility .
- getSwitchable() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
-
Get the switchoffAbility for a constraint.
- getSwitchable() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Get the switchable value (on, off, locked).
- getSwitchOff(String) - Method in class org.intermine.web.struts.TemplateForm
-
Get the SwitchOff ability.
- getSwitchOffAbility(PathConstraint) - Method in class org.intermine.template.TemplateQuery
-
Gets the sbitch-off-ability of a constraint.
- getSwitchOffAbility() - Method in class org.intermine.template.TemplateValue
-
Returns the SwitchOffAbility.
- getSynonym(Item, String) - Method in class org.intermine.bio.dataconversion.GFF3Converter
-
Create and add a synonym Item from the given information.
- getSynonymResultSet(Connection) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Return the interesting rows from the synonym table.
- getSynonyms() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
- getSynonyms(String, String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
-
For a particular primary identifier fetch a set of synonyms or return
null if id is not a primary identifier for the taxonId given.
- getSynonyms(String, String) - Method in class org.intermine.bio.dataconversion.IdResolver
-
For a particular primary identifier fetch a set of synonyms or return
null if id is not a primary identifier for the taxonId given.
- getSynonyms() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
used to assign sequences
- getSynonyms() - Method in class org.intermine.bio.ontology.OboTerm
-
Get a set of synonyms (Strings) for this term.
- getTable() - Method in class org.intermine.sql.query.Field
-
Returns the table of this field.
- getTable() - Method in class org.intermine.web.logic.results.DisplayField
-
Get the inline results table for this collection
- getTable() - Method in class org.intermine.web.struts.TableExportForm
-
Get the table identifier to look up the PagedTable in the servlet context
- getTableCount() - Method in class org.intermine.sql.precompute.BestQueryExplainer.Candidate
-
Returns the number of tables in this query.
- getTableDefinition() - Static method in class org.intermine.api.bag.SharingInvite
-
- getTableDefinition(Database, ClassDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
-
- getTableDisplayer() - Method in class org.intermine.web.logic.config.Type
-
Get the table Displayer
- getTableExportConfigs() - Method in class org.intermine.web.logic.config.WebConfig
-
Return a Map of TableExportConfig.id to TableExportConfig objects.
- getTableFieldConfigs() - Method in class org.intermine.web.logic.results.InlineResultsTable
-
- getTableFields(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.DatabaseSchema
-
Returns a Fields object of FieldDescriptors in the given table-mastering ClassDescriptor.
- getTableid() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
- getTableInfo(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Produces metadata for a given table, caching it to save time.
- getTableMaster(ClassDescriptor) - Method in class org.intermine.objectstore.intermine.DatabaseSchema
-
Returns the name of the table in which to store a row for the given ClassDescriptor.
- getTableName() - Method in class org.intermine.api.tracker.track.KeySearchTrack
-
- getTableName() - Method in class org.intermine.api.tracker.track.ListTrack
-
Return the table name where the track has to be saved
- getTableName() - Method in class org.intermine.api.tracker.track.LoginTrack
-
Return the table name where the track has to be saved
- getTableName() - Method in class org.intermine.api.tracker.track.QueryTrack
-
- getTableName() - Method in class org.intermine.api.tracker.track.TemplateTrack
-
Return the table name where the track has to be saved
- getTableName() - Method in interface org.intermine.api.tracker.track.Track
-
Return the table name where the track has to be saved
- getTableName(ClassDescriptor) - Static method in class org.intermine.sql.DatabaseUtil
-
Creates a table name for a class descriptor
- getTableSize(String, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterPostgresCopyImpl
-
Returns the approximate number of rows in a table.
- getTableSize(String, Connection) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
-
Returns the approximate number of rows in a table.
- getTabLink(String, TemplateQuery) - Method in class org.intermine.webservice.server.template.result.TemplateResultLinkGenerator
-
Returns link which gives results as lines, where values are tab separated.
- getTagById(int) - Method in class org.intermine.api.profile.TagManager
-
Get Tag by object id.
- getTagManager() - Method in interface org.intermine.api.API
-
- getTagManager() - Method in class org.intermine.api.InterMineAPI
-
- getTagManager() - Method in class org.intermine.api.profile.ProfileManager
-
Return the TagManager for adding, removing and fetching Tags assigned to templates, bags
and classes.
- getTagManager() - Method in class org.intermine.api.profile.TagManagerFactory
-
- getTagName() - Method in class org.intermine.api.search.TaggingEvent
-
- getTags(String, String, String, String) - Method in class org.intermine.api.profile.TagManager
-
Deprecated.
There are typed methods that are more suitable. Use them instead.
- getTags(ApiTemplate, Profile) - Method in class org.intermine.api.template.TemplateManager
-
For a (public or private) template, return all the tags.
- getTags(String) - Static method in class org.intermine.dwr.AjaxServices
-
Returns all tags of specified tag type together with prefixes of these tags.
- getTags() - Method in class org.intermine.webservice.client.lists.ItemList
-
Modifying the returned set will not change the underlying tags collection.
- getTags(ItemList) - Method in class org.intermine.webservice.client.services.ListService
-
Get the most current tag set for a list.
- getTags() - Method in class org.intermine.webservice.server.lists.ListInput
-
- getTagsByName(String, Profile, String) - Method in class org.intermine.api.profile.TagManager
-
Return all the tags with the given tag name, optionally filtered by tag-type.
- getTagsByType(String) - Method in class org.intermine.api.profile.TagManager
-
Return all tags of given type.
- getTagsForBag(InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager
-
Get a list of tags for a given bag.
- getTagString() - Method in class org.intermine.webservice.client.services.ListService.ListOperationInfo
-
Get the tags joined in the manner required for the list service.
- getTagType() - Method in class org.intermine.api.profile.StorableBag
-
- getTagType() - Method in interface org.intermine.api.profile.Taggable
-
Poly-Morphic Constant.
- getTagType() - Method in class org.intermine.api.template.ApiTemplate
-
- getTagValues() - Method in class org.intermine.bio.ontology.OboTerm
-
Gets the tagValues.
- getTarget() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the first value of the Target field from the attributes of this record.
- getTargetModel() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Return the Model that was passed to the constructor.
- getTargets() - Method in class org.intermine.webservice.client.widget.Widget
-
- getTargetType() - Method in class org.intermine.api.bag.AdditionalConverter
-
- getTaxonId() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
-
- getTaxonId(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
- getTaxonId() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getTaxonId() - Method in class org.intermine.bio.util.OrganismData
-
Get the taxonId of this organism.
- getTaxons() - Method in class org.intermine.bio.dataconversion.IdResolver
-
Return a set of taxon id.
- getTaxonsAndClassNames() - Method in class org.intermine.bio.dataconversion.IdResolver
-
Get a set of keys (taxon id + class name) resolver holds
- getTemplate(String) - Method in class org.intermine.api.profile.Profile
-
get a template
- getTemplate(Profile, String, String) - Method in class org.intermine.api.template.TemplateManager
-
Fetch a template with the scope provided, possible values are defined in Scope class.
- getTemplate(String) - Method in class org.intermine.webservice.client.services.TemplateService
-
Get the template with the given name, if accessible.
- getTemplateButton() - Method in class org.intermine.web.struts.ModifyTemplateForm
-
- getTemplateLabel() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Get the template label.
- getTemplateManager() - Method in interface org.intermine.api.API
-
- getTemplateManager() - Method in class org.intermine.api.InterMineAPI
-
- getTemplateManager() - Static method in class org.intermine.api.query.PathQueryAPI
-
Returns the TemplateManager for access to global and user template queries.
- getTemplateName() - Method in class org.intermine.api.tracker.track.TemplateTrack
-
Return the template name
- getTemplateNames() - Method in class org.intermine.webservice.client.services.TemplateService
-
Get the names of the templates to which the current user has access.
- getTemplates() - Method in class org.intermine.web.search.KeywordSearchResult
-
templates associated with this class
- getTemplates() - Method in class org.intermine.webservice.client.services.TemplateService
-
Get the templates to which the current user has access.
- getTemplateService() - Method in class org.intermine.webservice.client.core.ServiceFactory
-
Return a new QueryService for getting query results from.
- getTemplatesForType(String) - Method in class org.intermine.webservice.client.services.TemplateService
-
Get all the templates with constraints which constrain paths of a certain type.
- getTemplateSummariser() - Method in interface org.intermine.api.API
-
- getTemplateSummariser() - Method in class org.intermine.api.InterMineAPI
-
- getTemplateTracker() - Method in class org.intermine.api.tracker.TrackerDelegate
-
Return the tracker template
- getTemplateTracksPercentage(String) - Method in class org.intermine.dwr.TrackAjaxServices
-
- getTemplateTracksTrend() - Method in class org.intermine.dwr.TrackAjaxServices
-
- getTemporaryListName() - Method in class org.intermine.webservice.server.lists.ListInput
-
- getTermIdNameMap(Reader) - Method in class org.intermine.bio.ontology.OboParser
-
Parse an OBO file to produce a map from ontology term id to name.
- getTestCount() - Method in interface org.intermine.web.logic.widget.EnrichmentInput
-
The test count represents the number of tests that will be performed.
- getTestCount() - Method in class org.intermine.web.logic.widget.EnrichmentInputWidgetLdr
-
- getText() - Method in class org.intermine.web.logic.config.HeaderConfigLink
-
- getText() - Method in class org.intermine.web.logic.TreeNode
-
Get the text that was passed to the constructor
- getText() - Method in class org.intermine.web.struts.BuildBagForm
-
Get the text string
- getTextToFind() - Method in class org.intermine.web.struts.FindInListForm
-
- getTgtLocation() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Return the tgtLocation Item set by setTgtLocation()
- getTgtModel() - Method in class org.intermine.bio.dataconversion.GFF3Converter
-
Return the
- getTgtOrganism() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Return the tgtOrganism Item set by setTgtOrganism()
- getTgtSequence() - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Get the target Sequence Item set by setTgtSequence().
- getThickEnd() - Method in class org.intermine.bio.io.bed.BEDRecord
-
- getThickEnd() - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- getThickStart() - Method in class org.intermine.bio.io.bed.BEDRecord
-
- getThickStart() - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- getTickleCount() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
-
Find out how many times tickle has been called.
- getTileName() - Method in class org.intermine.web.logic.aspects.Aspect
-
Get the name of tile/page to embed in the centre of the data set homepage
- getTime() - Method in class org.intermine.sql.query.DummyExplainResult
-
Returns an estimate of the time it will take to complete the query.
- getTime() - Method in class org.intermine.sql.query.ExplainResult
-
Returns an estimate of the time it will take to complete the query.
- getTimeLimit() - Method in class org.intermine.sql.precompute.QueryOptimiserContext
-
Returns the time limit.
- getTimestamp() - Method in class org.intermine.api.tracker.track.TrackAbstract
-
Return the timestamp of the event
- getTitle() - Method in class org.intermine.api.bag.AdditionalConverter
-
- getTitle() - Method in class org.intermine.api.profile.InterMineBag
-
The user-friendly title for this object.
- getTitle() - Method in class org.intermine.api.profile.InvalidBag
-
- getTitle() - Method in interface org.intermine.api.search.WebSearchable
-
The user-friendly title for this object.
- getTitle() - Method in class org.intermine.pathquery.PathQuery
-
Gets the title for this query.
- getTitle() - Method in class org.intermine.template.TemplateQuery
-
- getTitle() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Return the last class in the path and fieldname as the title for the constraint.
- getTitle() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- getTitle() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
-
Get the title
- getTitle() - Method in class org.intermine.web.logic.widget.Widget
-
Get the widget title
- getTitle() - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
title of the widget
- getTitle() - Method in class org.intermine.web.struts.TemplateSettingsForm
-
Return the title
- getTitle() - Method in class org.intermine.webservice.client.widget.Widget
-
- getTitleMain() - Method in class org.intermine.web.logic.results.ReportObject
-
Used by JSP
- getTitles() - Method in class org.intermine.web.logic.config.HeaderConfigTitle
-
- getTitleSub() - Method in class org.intermine.web.logic.results.ReportObject
-
Used by JSP
- getToggledElements() - Static method in class org.intermine.dwr.AjaxServices
-
This method gets a map of ids of elements that were in the past (during session) toggled and
returns them in JSON
- getToggledElements() - Method in class org.intermine.web.logic.results.WebState
-
Gets map of ids of elements that were in the past (during session) toggled
- if they are opened or closed.
- getToken() - Method in class org.intermine.api.bag.SharingInvite
-
- getToken() - Method in class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
-
- getToken() - Method in class org.intermine.web.struts.PasswordResetForm
-
Gets the value of token.
- getToken() - Method in class org.intermine.webservice.server.user.DeletionTokenInfoService
-
- getTokenUrl() - Method in class org.intermine.web.struts.oauth2.CustomOAuthProvider
-
- getTokenUrl() - Method in class org.intermine.web.struts.oauth2.DefaultOAuthProvider
-
- getTokenUrl() - Method in interface org.intermine.web.struts.oauth2.OAuthProvider
-
- getTotalHits() - Method in class org.intermine.api.lucene.ResultsWithFacets
-
- getTracker(String, Connection, Queue<Track>) - Static method in class org.intermine.api.tracker.factory.TrackerFactory
-
Return the tracker instantiated with the reflection
- getTracker(String) - Method in class org.intermine.api.tracker.TrackerDelegate
-
Return the tracker specified in input
- getTrackerDelegate() - Method in interface org.intermine.api.API
-
- getTrackerDelegate() - Method in class org.intermine.api.InterMineAPI
-
- getTrackers() - Method in class org.intermine.api.tracker.TrackerDelegate
-
Return the trackers saved in the TrackerManager
- getTrackTableName() - Method in class org.intermine.api.tracker.AbstractTracker
-
Return the table's name associated to the tracker
- getTrail() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
-
Get the trail URL parameter for this trail element.
- getTransitiveOver() - Method in class org.intermine.bio.ontology.OboTypeDefinition
-
- getTranslator() - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
-
Returns the Translator associated with the underlying ObjectStoreTranslatingImpl.
- getTranslator() - Method in class org.intermine.objectstore.translating.ObjectStoreTranslatingImpl
-
Return the Translator that was passed to the constructor.
- getType() - Method in class org.intermine.api.bag.BagQueryUpgrade
-
- getType() - Method in class org.intermine.api.beans.ObjectDetails
-
- getType() - Method in interface org.intermine.api.idresolution.Job
-
- getType() - Method in interface org.intermine.api.idresolution.JobInput
-
- getType() - Method in class org.intermine.api.idresolution.ResolutionJob
-
- getType() - Method in class org.intermine.api.idresolution.UpgradeJob
-
- getType() - Method in class org.intermine.api.lucene.KeywordSearchFacetData
-
type of facet
- getType() - Method in class org.intermine.api.profile.InterMineBag
-
Get the type of this bag (a class from InterMine model)
- getType() - Method in class org.intermine.api.profile.InvalidBag
-
- getType() - Method in class org.intermine.api.profile.StorableBag
-
Get the unqualified name of class that the objects in this bag represent.
- getType() - Method in class org.intermine.api.results.Column
-
Return the type of this Column
- getType() - Method in interface org.intermine.api.results.ResultCell
-
- getType() - Method in class org.intermine.api.results.ResultElement
-
Get the type
- getType() - Method in class org.intermine.api.tracker.track.ListTrack
-
Return the class type of items contained into the list
- getType() - Method in class org.intermine.bio.dataconversion.UniprotEntry.Dbref
-
- getType() - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Return the type field of this record.
- getType() - Method in class org.intermine.bio.ontology.OboTermSynonym
-
Get the synonym type.
- getType(FieldDescriptor) - Method in class org.intermine.codegen.JavaModelOutput
-
Return the java type of a particular field.
- getType() - Method in class org.intermine.dataloader.Source
-
- getType() - Method in class org.intermine.objectstore.query.Clob
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.ObjectStoreBag
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.ObjectStoreBagCombination
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.OrderDescending
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.PathExpressionField
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.QueryCast
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.QueryClass
-
Gets the Java class represented by this QueryClass
- getType() - Method in class org.intermine.objectstore.query.QueryClassBag
-
Gets the Java class represented by this QueryClassBag.
- getType() - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.QueryCollectionReference
-
Gets the Java class of this QueryReference.
- getType() - Method in class org.intermine.objectstore.query.QueryExpression
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.QueryField
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.QueryForeignKey
-
Gets the Java class of this QueryReference.
- getType() - Method in class org.intermine.objectstore.query.QueryFunction
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.QueryObjectReference
-
Gets the Java class of this QueryReference.
- getType() - Method in interface org.intermine.objectstore.query.QueryOrderable
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.QueryReference
-
Gets the Java class of this QueryReference.
- getType() - Method in interface org.intermine.objectstore.query.QuerySelectable
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.QueryValue
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.objectstore.query.WidthBucketFunction
-
Get Java type represented by this item.
- getType() - Method in class org.intermine.pathquery.Node
-
Gets the value of type
- getType(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
-
A static method to get the type of this constraint if it is a
sub-class constraint, or otherwise return null.
- getType() - Method in class org.intermine.pathquery.PathConstraintSubclass
-
Returns the class that the constraint is constraining to.
- getType() - Method in class org.intermine.web.logic.bag.WebJobInput
-
- getType() - Method in class org.intermine.web.logic.querybuilder.DisplayPath
-
Returns the type of the value represented by this path, as a string.
- getType() - Method in class org.intermine.web.logic.results.ReportObject
-
Get the unqualified class name for the report object.
- getType() - Method in class org.intermine.web.logic.WebUtil.HeadResource
-
- getType() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
-
- getType() - Method in class org.intermine.web.search.KeywordSearchResult
-
returns the name of the class for this object (category)
- getType() - Method in class org.intermine.web.struts.BuildBagForm
-
Get the bag type
- getType() - Method in class org.intermine.web.struts.CSVExportForm
-
Return the export type: "tab", etc.
- getType() - Method in class org.intermine.web.struts.ObjectTrailController.TrailElement
-
Return whether or not this trail element refers to a table.
- getType() - Method in class org.intermine.web.struts.TableExportForm
-
Return the export type: "tab", etc.
- getType() - Method in class org.intermine.web.tags.disclosure.DisclosureTag
-
Returns type of tag.
- getType() - Method in class org.intermine.webservice.client.core.ContentType
-
- getType() - Method in interface org.intermine.webservice.client.core.Request
-
- getType() - Method in class org.intermine.webservice.client.core.RequestImpl
- getType() - Method in class org.intermine.webservice.client.lists.ItemList
-
- getType() - Method in class org.intermine.webservice.client.results.Item
-
Get the type of this object.
- getType() - Method in class org.intermine.webservice.server.core.TableCell
-
- getType() - Method in class org.intermine.webservice.server.lists.ListInput
-
- getType() - Method in class org.intermine.webservice.server.lists.ListsServiceInput
-
- getTypeClass() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- getTypeClsString() - Method in class org.intermine.api.results.Column
-
Get the column type unqualified as a String
- getTypeForColumn(int) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Return the class from the data model for the data displayed in indexed column.
- getTypes() - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Get the comma separated unqualified class names for which this displayer should be displayed.
- getTypes() - Method in class org.intermine.web.logic.config.WebConfig
-
Get a map from fully qualified class name to the Type config for that class
- getUid() - Method in interface org.intermine.api.idresolution.Job
-
- getUid() - Method in class org.intermine.api.idresolution.ResolutionJob
-
- getUid() - Method in class org.intermine.api.idresolution.UpgradeJob
-
- getUnencodedUrl() - Method in interface org.intermine.webservice.client.core.Request
-
- getUnencodedUrl() - Method in class org.intermine.webservice.client.core.RequestImpl
-
- getUnformatted() - Method in class org.intermine.web.logic.results.ReportObject.TitleValue
-
Get the unformatted version that is just the field value.
- getUnion() - Method in class org.intermine.sql.query.Query
-
Returns the List of queries in the UNION set of this query.
- getUniprot() - Method in class org.intermine.bio.util.OrganismData
-
- getUniprotAccession() - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- getUniqueIdentifier() - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
-
eg. primaryIdentifier
- getUniqueIdentifier(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig
-
- getUniqueInteger(Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Return a unique integer from a SEQUENCE in the database.
- getUniqueItemId(String) - Method in class org.intermine.dataconversion.DataConverter
-
List of unique identifiers and their refIds.
- getUnmatchedIdentifiers() - Method in class org.intermine.webservice.client.lists.ItemList
-
Get the identifiers used in creating or appending to this list that
could not be resolved to any objects.
- getUnqualifiedClassName() - Method in class org.intermine.web.logic.config.Type
-
- getUnresolved() - Method in class org.intermine.api.bag.BagQueryResult
-
Deprecated.
Use getUnresolvedIdentifiers
- getUnresolvedIdentifiers() - Method in class org.intermine.api.bag.BagQueryResult
-
Get all the unresolved identifiers.
- getUnusedListName() - Method in class org.intermine.webservice.client.services.ListService.ListOperationInfo
-
Get a name for the list if none has been supplied.
- getUpdatedPathQuery() - Method in class org.intermine.api.profile.PathQueryUpdate
-
Return a new pathquery updated to the new model
- getUrl() - Method in class org.intermine.api.mines.LocalMine
-
- getUrl() - Method in interface org.intermine.api.mines.Mine
-
- getUrl() - Method in class org.intermine.api.mines.RemoteMine
-
- getURL() - Method in class org.intermine.sql.Database
-
Gets the URL from this database
- getUrl() - Method in class org.intermine.web.logic.aspects.AspectSource
-
Get the URL back to source website.
- getUrl() - Method in class org.intermine.web.logic.config.HeaderConfigLink
-
- getUrl() - Method in class org.intermine.web.logic.WebUtil.HeadResource
-
- getUrl() - Method in class org.intermine.webservice.client.core.Service
-
Returns service URL
Example: http://www.flymine.org/query/service/query/results
- getUrlField() - Method in class org.intermine.api.bag.AdditionalConverter
-
- getUseBagConstraint(String) - Method in class org.intermine.web.struts.TemplateForm
-
Get the value of useBagConstraint for given constraint key.
- getUseJoin() - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
- getUser() - Method in class org.intermine.sql.Database
-
Gets the username for this Database
- getUserAndGlobalTemplates(Profile) - Method in class org.intermine.api.template.TemplateManager
-
Fetch all user and global templates in a single map for the given user.
- getUserBag(Profile, String) - Method in class org.intermine.api.bag.BagManager
-
Fetch a user bag by name.
- getUserBags(Profile) - Method in class org.intermine.api.bag.BagManager
-
Fetch bags for the given profile.
- getUserBagsContainingId(Profile, Integer) - Method in class org.intermine.api.bag.BagManager
-
Fetch user bags that contain the given id.
- getUserBagsWithTag(Profile, String) - Method in class org.intermine.api.bag.BagManager
-
Fetch bags from given protocol with a particular tag assigned to them.
- getUserBagsWithTags(Profile, List<String>) - Method in class org.intermine.api.bag.BagManager
-
Give me profile bags matching a set of tags
- getUserId() - Method in class org.intermine.api.profile.Profile
-
Get the value of userId
- getUserLogin(Connection) - Method in class org.intermine.api.tracker.LoginTracker
-
Return the number of access for each user
- getUserLogin() - Method in class org.intermine.api.tracker.TrackerDelegate
-
Return the number of access for each user
- getUsername() - Method in class org.intermine.api.profile.Profile
-
Get the value of username
- getUserName() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
-
The name of the user logged in when this info was generated
- getUserName() - Method in class org.intermine.api.tracker.track.TrackAbstract
-
Return the user name
- getUsername() - Method in class org.intermine.api.util.AnonProfile
-
- getUsername() - Method in class org.intermine.web.struts.CreateAccountForm
-
- getUsername() - Method in class org.intermine.web.struts.LoginForm
-
Gets the value of username
The user name is always returned in LOWER CASE.
- getUsername() - Method in class org.intermine.web.struts.RequestPasswordForm
-
Gets the value of username
- getUserName() - Method in class org.intermine.webservice.server.WebServiceInput
-
- getUsernameForToken(String) - Method in class org.intermine.api.profile.ProfileManager
-
Returns the username associated with the given token, if the token is valid.
- getUserOrGlobalTemplate(Profile, String) - Method in class org.intermine.api.template.TemplateManager
-
Fetch a user or global template by name.
- getUserProfile() - Method in class org.intermine.api.InterMineAPI
-
- getUserProfile(String) - Method in class org.intermine.api.profile.ProfileManager
-
Perform a query to retrieve a user's backing UserProfile
- getUserProfile(Integer) - Method in class org.intermine.api.profile.ProfileManager
-
Perform a query to retrieve a user's backing UserProfile
- getUserProfileWriter() - Method in class org.intermine.api.profile.InterMineBag
-
- getUserProfileWriter() - Method in class org.intermine.api.profile.InvalidBag
-
- getUserProfileWriter() - Method in class org.intermine.api.profile.StorableBag
-
Get a reference to a connection to the database where user data is persisted.
- getUsersSharingBag(String, String) - Method in class org.intermine.api.bag.BagManager
-
Return the users sharing the list given in input, not the owner
- getUsersSharingBag(String) - Method in class org.intermine.dwr.AjaxServices
-
Return the list of users who have access to this bag because it has been
shared with them.
- getUsersWithAccessToBag(StorableBag) - Method in class org.intermine.api.bag.SharedBagManager
-
Return the users this bag is shared with.
- getUserTagNames(String, Profile) - Method in class org.intermine.api.profile.TagManager
-
Returns names of tags of specified user and tag type.
- getUserTagNames(String, String) - Method in class org.intermine.api.profile.TagManager
-
Deprecated.
It is better to use the typed methods instead.
- getUserTags(String) - Method in class org.intermine.api.profile.TagManager
-
Returns tags of specified user.
- getUserTags(Profile) - Method in class org.intermine.api.profile.TagManager
-
Returns tags of specified user.
- getUserTemplate(Profile, String) - Method in class org.intermine.api.template.TemplateManager
-
Fetch a user template by name.
- getUserToken() - Method in class org.intermine.api.query.codegen.WebserviceCodeGenInfo
-
A token for the user.
- getUserWithUniqueMapping(String, String) - Method in class org.intermine.api.profile.PreferencesManager
-
- getUUID() - Method in class org.intermine.webservice.server.user.DeletionToken
-
- getValidGlobalTemplates() - Method in class org.intermine.api.template.TemplateManager
-
Return a map from template name to template query containing superuser templates that are
tagged as public and are valid for the current data model.
- getValidOps() - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Given the path being constrained return the valid constraint operations.
- getValidRangeTargets() - Static method in class org.intermine.api.query.MainHelper
-
- getValue() - Method in class org.intermine.api.lucene.KeywordSearchFacet
-
selected value
- getValue() - Method in class org.intermine.api.profile.BagValue
-
- getValue() - Method in class org.intermine.api.results.flatouterjoins.MultiRowFirstValue
-
Returns the value of the entry.
- getValue() - Method in class org.intermine.api.results.flatouterjoins.MultiRowLaterValue
-
Returns the value of the entry.
- getValue() - Method in class org.intermine.api.results.flatouterjoins.MultiRowValue
-
Returns the value of the entry.
- getValue() - Method in class org.intermine.bio.dataconversion.UniprotConfig.IdentifierConfig
-
- getValue() - Method in class org.intermine.bio.dataconversion.UniprotEntry.Dbref
-
- getValue() - Method in class org.intermine.objectstore.query.ObjectStoreBagsForObject
-
Returns the value.
- getValue() - Method in class org.intermine.objectstore.query.QueryCast
-
Returns the QueryEvaluable that is the actual value.
- getValue() - Method in class org.intermine.objectstore.query.QueryValue
-
Returns the object that is the actual value.
- getValue() - Method in class org.intermine.objectstore.query.UnknownTypeValue
-
Returns the value.
- getValue(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
-
A static method for accessing values without having to handle
the subclasses manually.
- getValue() - Method in class org.intermine.pathquery.PathConstraintAttribute
-
Returns the value that the constraint is constraining to.
- getValue() - Method in class org.intermine.pathquery.PathConstraintLookup
-
Returns the lookup value for this constraint.
- getValue() - Method in class org.intermine.sql.query.OrderDescending
-
Returns the value.
- getValue() - Method in class org.intermine.sql.query.SelectValue
-
Gets the AbstractValue from this object.
- getValue() - Method in class org.intermine.template.TemplateValue
-
Returns value.
- getValue() - Method in class org.intermine.web.logic.config.InlineListObject
-
Fetch the column value, ie "Zerknullt" for Synonyms of a Gene
- getValue() - Method in class org.intermine.web.logic.querybuilder.SummaryConstraint
-
Get a string representation of the constraint value to be displayed.
- getValue() - Method in class org.intermine.web.logic.results.ReportObjectField
-
Get field value
- getValue() - Method in class org.intermine.web.logic.template.ConstraintInput
-
Returns constraint value.
- getValue() - Method in class org.intermine.webservice.client.template.TemplateParameter
-
Returns value.
- getValue() - Method in class org.intermine.webservice.server.core.Pair
-
- getValue() - Method in class org.intermine.xml.full.Attribute
-
Get the value of this field
- getValueHasDisplayer() - Method in class org.intermine.web.logic.results.ReportObjectField
-
Does the field have a custom displayer defined for the value?
- getValueMap() - Method in class org.intermine.sql.precompute.PrecomputedTable
-
Gets a Map from AbstractValue to SelectValue for the Query in this PrecomputedTable.
- getValues(String) - Method in class org.intermine.dataloader.EquivalentObjectHints
-
Returns a Set of values that were in the database for a particular class and fieldname.
- getValues(PathConstraint) - Static method in class org.intermine.pathquery.PathConstraint
-
Get the values for a constraint.
- getValues() - Method in class org.intermine.pathquery.PathConstraintMultiValue
-
Returns the value collection that the constraint is constraining to.
- getValues() - Method in class org.intermine.template.TemplateValue
-
- getValues() - Method in class org.intermine.webservice.client.template.TemplateParameter
-
- getValuesForField(String) - Method in class org.intermine.web.autocompletion.LuceneObjectClass
-
getValuesForField
- getValuesForField(String, int) - Method in class org.intermine.web.autocompletion.LuceneObjectClass
-
getValuesForField
- getValuesFromInput(TemplateQuery, TemplateResultInput) - Static method in class org.intermine.web.logic.template.Templates
-
Creates a map from input to be used later to populate the template.
- getVariableNames() - Method in class org.intermine.pathquery.LogicExpression
-
Get the Set of variable names.
- getVerboseQueryLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Gets the verboseQueryLog configuration option.
- getVerboseQueryLog() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Gets the verboseQueryLog configuration option.
- getVersion() - Method in class org.intermine.api.profile.ProfileManager
-
Returns the version number of the data format in the database for this ProfileManager.
- getVersion() - Method in class org.intermine.objectstore.intermine.DatabaseSchema
-
Returns the database format version.
- getVersion() - Method in class org.intermine.sql.Database
-
Get the version number of the database as a string.
- getVersion() - Method in class org.intermine.webservice.client.core.Service
-
- getView() - Method in class org.intermine.pathquery.PathQuery
-
Returns the current view list.
- getView() - Method in class org.intermine.web.struts.TemplateForm
-
Get the selected alternative view name.
- getViewPaths() - Method in class org.intermine.api.results.ExportResultsIterator
-
- getViews() - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- getVisibleColumnCount() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Return the number of visible columns.
- getVisibleIndexes() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Returns indexes of columns, that should be displayed.
- getWarnings() - Method in class org.intermine.webservice.server.query.result.XMLValidator
-
Returns warnings occurred during parsing xml.
- getWarnings() - Method in class org.intermine.webservice.server.query.result.XMLValidatorErrorHandler
-
Returns warning occurred during parsing xml.
- getWebConfig() - Static method in class org.intermine.web.context.InterMineContext
-
- getWebConfig(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
-
- getWebConfig(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
-
- getWebConfig() - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
- getWebProperties() - Static method in class org.intermine.web.context.InterMineContext
-
- getWebProperties(ServletContext) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Returns the web properties.
- getWebProperties(HttpServletRequest) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Returns the web properties.
- getWebProperties(HttpServletRequest) - Static method in class org.intermine.web.struts.InterMineAction
-
Get the web proprties.
- getWebResultsExecutor(Profile) - Method in interface org.intermine.api.API
-
- getWebResultsExecutor(Profile) - Method in class org.intermine.api.InterMineAPI
-
- getWebSearchableMap(String) - Method in class org.intermine.api.search.GlobalRepository
-
Get a map from name -> object for all the websearchables of the given type.
- getWebSearchableMap(String) - Method in class org.intermine.api.search.SearchRepository
-
Get a map from name -> object for all the websearchables of the given type.
- getWebSearchablesByType(String) - Method in class org.intermine.api.profile.Profile
-
Return a WebSearchable Map for the given type.
- getWebState(HttpSession) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Get WebState object that is used for saving state of webapp GUI.
- getWebTable() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
- getWhere() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- getWhere() - Method in class org.intermine.sql.query.Query
-
Gets the Set of constraints in the where clause of this query.
- getWhereBuffer() - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- getWhichInput() - Method in class org.intermine.web.struts.BuildBagForm
-
Get the method the user used to upload the bag.
- getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
- getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig
-
- getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
- getWidget(InterMineBag, InterMineBag, ObjectStore, WidgetOptions) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- getWidget(String) - Method in class org.intermine.webservice.client.services.WidgetService
-
- getWidgetid() - Method in class org.intermine.web.struts.WidgetForm
-
- getWidgetId() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
-
Get the name or id of the widget
- getWidgets() - Method in class org.intermine.web.logic.config.Type
-
- getWidgets() - Method in class org.intermine.web.logic.config.WebConfig
-
- getWidgets() - Method in class org.intermine.webservice.client.services.WidgetService
-
- getWidgetService() - Method in class org.intermine.webservice.client.core.ServiceFactory
-
Return the WidgetService for retrieving widget information.
- getWidgetTitle() - Method in class org.intermine.web.struts.WidgetForm
-
used on results page for description: "results for widget XYZ"
- getWidgetTotal() - Method in interface org.intermine.web.logic.widget.DataSetLdr
-
This method is used to calculate the 'not analysed' total displayed on each widget
- getWidgetTotal() - Method in class org.intermine.web.logic.widget.GraphWidgetLoader
-
- getWidgetTotal() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
-
- getWidgetType() - Method in class org.intermine.webservice.client.widget.Widget
-
- getWidgetType(WidgetConfig) - Method in class org.intermine.webservice.server.widget.WidgetProcessorImpl
-
- getWidth() - Method in class org.intermine.sql.query.ExplainResult
-
Returns the width of the data returned by the database for this query.
- getWildCards() - Method in interface org.intermine.api.idresolution.JobInput
-
- getWildCards() - Method in class org.intermine.web.logic.bag.WebJobInput
-
- getWithinOptions() - Method in class org.intermine.api.query.range.AbstractHelper
-
- getWorkingTemplates(Profile) - Method in class org.intermine.api.template.TemplateManager
-
Fetch all user and global templates that are valid.
- getWorkingTemplates() - Method in class org.intermine.api.template.TemplateManager
-
Fetch all global templates that are valid.
- getWormIdResolver() - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a worm id resolver
- getWormIdResolver(String) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a worm id resolver
- getWormIdResolver(String, boolean) - Static method in class org.intermine.bio.dataconversion.IdResolverService
-
Create a worm id resolver
- getWriter() - Method in class org.intermine.webservice.server.output.StreamedOutput
-
Returns associated writer
- getWrittenResultsCount() - Method in interface org.intermine.web.logic.export.Exporter
-
- getWrittenResultsCount() - Method in class org.intermine.web.logic.export.ExporterImpl
- getXAxisLabel() - Method in class org.intermine.webservice.client.widget.Widget
-
- getXml() - Method in class org.intermine.web.struts.ImportTagsForm
-
Get the xml.
- getXml() - Method in class org.intermine.web.struts.ImportXMLForm
-
Get the xml.
- getXML() - Method in class org.intermine.webservice.server.query.QueryUploadService
-
Get the XML which represents the queries to be saved.
- getXml() - Method in class org.intermine.webservice.server.query.result.QueryResultInput
-
Gets xml query string.
- getXMLSchemaUrl() - Method in class org.intermine.webservice.server.query.AbstractQueryService
-
- getXref() - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
-
- getXrefs() - Method in class org.intermine.bio.dataconversion.EntrezGeneIdResolverFactory
-
used for testing
- getXrefs() - Method in class org.intermine.bio.ontology.OboTerm
-
Get a set of xrefs (OboTerms) for this term.
- getYAxisLabel() - Method in class org.intermine.webservice.client.widget.Widget
-
- GFF3Converter - Class in org.intermine.bio.dataconversion
-
Class to read a GFF3 source data and produce a data representation
- GFF3Converter(ItemWriter, String, String, String, String, Model, GFF3RecordHandler, GFF3SeqHandler) - Constructor for class org.intermine.bio.dataconversion.GFF3Converter
-
Constructor
- GFF3ConverterTask - Class in org.intermine.bio.task
-
Task to convert gff3 data
- GFF3ConverterTask() - Constructor for class org.intermine.bio.task.GFF3ConverterTask
-
- GFF3Parser - Class in org.intermine.bio.io.gff3
-
A parser for GFF3 files.
- GFF3Record - Class in org.intermine.bio.io.gff3
-
A class that represents one line of a GFF3 file.
- GFF3Record(String) - Constructor for class org.intermine.bio.io.gff3.GFF3Record
-
Create a GFF3Record from a line of a GFF3 file
- GFF3Record(String, String, String, int, int, Double, String, String, Map<String, List<String>>) - Constructor for class org.intermine.bio.io.gff3.GFF3Record
-
Create a new GFF3Record
- GFF3RecordHandler - Class in org.intermine.bio.dataconversion
-
Permits specific operations to be performed when processing an line of GFF3.
- GFF3RecordHandler(Model) - Constructor for class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Construct with the model to create items in (for type checking).
- GFF3SeqHandler - Class in org.intermine.bio.dataconversion
-
An interface used by GFF3Converter to choose the type of sequence Items.
- GFF3SeqHandler() - Constructor for class org.intermine.bio.dataconversion.GFF3SeqHandler
-
- GFF3Util - Class in org.intermine.bio.web.export
-
Utility methods for GFF3.
- GLOBAL - Static variable in class org.intermine.api.search.Scope
-
Global scope for public bags, templates, etc.
- GLOBAL_BAGS - Static variable in class org.intermine.api.search.SearchTarget
-
The search target for global bags
- GLOBAL_CACHE - Static variable in class org.intermine.web.logic.Constants
-
Servlet attribute.
- GLOBAL_SEARCH_REPOSITORY - Static variable in class org.intermine.web.logic.Constants
-
Servlet attribute.
- GLOBAL_TEMPLATES - Static variable in class org.intermine.api.search.SearchTarget
-
The search target for global templates
- GlobalRepository - Class in org.intermine.api.search
-
A representation of an object that knows how to index global objects, and also how to respond
to changes to those objects.
- GlobalRepository(Profile) - Constructor for class org.intermine.api.search.GlobalRepository
-
Build a new global search repository and register it with the list of global repositories
available.
- GLOBALS - Static variable in class org.intermine.api.search.SearchRepository
-
- GoConverter - Class in org.intermine.bio.dataconversion
-
DataConverter to parse a go annotation file into Items
- GoConverter(ItemWriter, Model) - Constructor for class org.intermine.bio.dataconversion.GoConverter
-
Constructor
- goFaster() - Method in class org.intermine.api.results.ExportResultsIterator
-
Switches on the goFaster mode in the objectstore for this query.
- goFaster() - Method in class org.intermine.api.results.WebResults
-
Calls ObjectStore.goFaster() if this object wraps a Results object from an
ObjectStoreInterMineImpl.
- goFaster(Query) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Makes a certain Query go faster, using extra resources.
- goFasterCacheMap - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- goFasterCountMap - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- goFasterMap - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- goFasterWithConnection(Query, Connection) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Makes a certain Query go faster, using extra resources.
- GoPostprocess - Class in org.intermine.bio.postprocess
-
Take any GOAnnotation objects assigned to proteins and copy them to corresponding genes.
- GoPostprocess(ObjectStoreWriter) - Constructor for class org.intermine.bio.postprocess.GoPostprocess
-
Create a new UpdateOrthologes object from an ObjectStoreWriter
- GORNULL - Static variable in class org.intermine.sql.query.Constraint
-
An operation for this constraint indicating that the left is greater than the right, or
the left is null.
- goTerms - Variable in class org.intermine.bio.dataconversion.GoConverter
-
- GotoWebSearchableAction - Class in org.intermine.web.struts
-
Action handles search.
- GotoWebSearchableAction() - Constructor for class org.intermine.web.struts.GotoWebSearchableAction
-
- grant(Database, String, String) - Static method in class org.intermine.sql.DatabaseUtil
-
Grant permission on all tables for given user on specified database.
- grantPermission(String, String, Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.profile.ProfileManager
-
Grant permission to the given identity, creating a profile for this
identity if it is not already available.
- GrantTask - Class in org.intermine.task
-
Task to grant permissions on all tables in a database to a given user.
- GrantTask() - Constructor for class org.intermine.task.GrantTask
-
- GRAPH_CACHE - Static variable in class org.intermine.web.logic.Constants
-
Servlet attribute.
- GraphJSONProcessor - Class in org.intermine.webservice.server.widget
-
A widget result processor that produces chart results in JSON.
- GraphService - Class in org.intermine.webservice.server.widget
-
- GraphService(InterMineAPI) - Constructor for class org.intermine.webservice.server.widget.GraphService
-
- GraphWidget - Class in org.intermine.web.logic.widget
-
- GraphWidget(GraphWidgetConfig, InterMineBag, ObjectStore, WidgetOptions) - Constructor for class org.intermine.web.logic.widget.GraphWidget
-
- GraphWidget.DivNumberFormat - Class in org.intermine.web.logic.widget
-
class used to format the p-values on the graph
- GraphWidget.DivNumberFormat(int) - Constructor for class org.intermine.web.logic.widget.GraphWidget.DivNumberFormat
-
- GraphWidgetActionType - Enum in org.intermine.web.logic.widget
-
Enumeration for possible actions when create the query for graph widgets.
- GraphWidgetConfig - Class in org.intermine.web.logic.widget.config
-
Configuration object describing details of a graph displayer
- GraphWidgetConfig() - Constructor for class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- GraphWidgetLoader - Class in org.intermine.web.logic.widget
-
The class that does the actual querying for results.
- GraphWidgetLoader(InterMineBag, ObjectStore, GraphWidgetConfig, String) - Constructor for class org.intermine.web.logic.widget.GraphWidgetLoader
-
Constructor.
- GraphWidgetsServlet - Class in org.intermine.webservice.server.widget
-
Servlet running WidgetsService.
- GraphWidgetsServlet() - Constructor for class org.intermine.webservice.server.widget.GraphWidgetsServlet
-
- GraphXMLProcessor - Class in org.intermine.webservice.server.widget
-
A processor for returning results from graph widgets in XML.
- GraphXMLProcessor() - Constructor for class org.intermine.webservice.server.widget.GraphXMLProcessor
-
Constructor, obvs
- GREATER - Static variable in class org.intermine.sql.query.AbstractValue
-
Describes one AbstractValue as being greater than another AbstractValue.
- greaterOrEqual(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
-
Compare this value of this AbstractValue with another to see if it is more or equal.
- greaterThan(String, String) - Static method in class org.intermine.pathquery.Constraints
-
Creates a constraint for a path to be greater than a value.
- greaterThan(AbstractValue, Map<AbstractTable, AbstractTable>, Map<AbstractTable, AbstractTable>) - Method in class org.intermine.sql.query.AbstractValue
-
Compare this value of this AbstractValue with another to see if it is more.
- greaterThanEqualTo(String, String) - Static method in class org.intermine.pathquery.Constraints
-
Creates a constraint for a path to be greater than or equal to a value.
- GREATEST - Static variable in class org.intermine.objectstore.query.QueryExpression
-
Return the greatest value from two expressions, e.g.
- GREATEST - Static variable in class org.intermine.sql.query.Function
-
GREATEST(x, y) - takes two operands
- groupBy - Variable in class org.intermine.sql.query.Query
-
- groupByClass(Collection<E>, boolean) - Static method in class org.intermine.util.CollectionUtil
-
Sorts objects in the given collection into different types by Class.
- SAFENESS_ANTISAFE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
-
Safeness value indicating a situation safe for ContainsConstraint DOES NOT CONTAIN
- SAFENESS_SAFE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
-
Safeness value indicating a situation safe for ContainsConstraint CONTAINS
- SAFENESS_UNSAFE - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
-
Safeness value indicating a situation unsafe for ContainsConstraint
- save() - Method in class org.intermine.api.bag.SharingInvite
-
- save(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ModifyQueryChangeAction
-
Save a query from the history.
- saveBag(InterMineBag) - Method in class org.intermine.api.profile.Profile
-
Stores a new bag in the profile.
- saveBag(String, InterMineBag) - Method in class org.intermine.api.profile.Profile
-
Stores a new bag in the profile.
- saveBag(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.SaveBagAction
-
Save the selected objects to a bag on the session
- SaveBagAction - Class in org.intermine.web.struts
-
Saves selected items in a new bag or combines with existing bag.
- SaveBagAction() - Constructor for class org.intermine.web.struts.SaveBagAction
-
- saveBagDescription(String, String) - Method in class org.intermine.dwr.AjaxServices
-
For a given bag, set its description
- SaveBagForm - Class in org.intermine.web.struts
-
Form bean for the results table and bag creation form.
- SaveBagForm() - Constructor for class org.intermine.web.struts.SaveBagForm
-
Constructor
- saveClassKeys(String, File) - Static method in class org.intermine.modelproduction.MetadataManager
-
Save the class keys, in serialized form, to the specified directory
- SAVED_BAG_STATUS - Static variable in class org.intermine.web.logic.Constants
-
key for the map saved in the session containing the status of saved bags
- savedBagId - Variable in class org.intermine.api.profile.StorableBag
-
- savedBags - Variable in class org.intermine.api.profile.Profile
-
- savedCounts - Variable in class org.intermine.dataloader.HintingFetcher
-
- savedInvalidBags - Variable in class org.intermine.api.profile.Profile
-
- savedQueries - Variable in class org.intermine.api.profile.Profile
-
- SavedQuery - Class in org.intermine.api.profile
-
Container for a saved query.
- SavedQuery(String, Date, PathQuery) - Constructor for class org.intermine.api.profile.SavedQuery
-
Construct a new instance of SavedQuery.
- SavedQueryBinding - Class in org.intermine.api.xml
-
Convert SavedQuerys to and from XML
- SavedQueryHandler - Class in org.intermine.api.xml
-
Extension of PathQueryHandler to handle parsing SavedQuerys
- SavedQueryHandler(Map<String, SavedQuery>, Map, int) - Constructor for class org.intermine.api.xml.SavedQueryHandler
-
Constructor
- SavedQueryRetrievalService - Class in org.intermine.webservice.server.query
-
- SavedQueryRetrievalService(InterMineAPI) - Constructor for class org.intermine.webservice.server.query.SavedQueryRetrievalService
-
- savedTemplateQuery - Variable in class org.intermine.api.template.ApiTemplate
-
SavedTemplateQuery object in the UserProfile database, so we can update summaries.
- savedTemplates - Variable in class org.intermine.api.profile.Profile
-
- savedTimes - Variable in class org.intermine.dataloader.HintingFetcher
-
- SaveFromIdsToBagAction - Class in org.intermine.web.struts
-
Saves selected items with InterMine ids and a Type in a new bag or combines
with existing bag.
- SaveFromIdsToBagAction() - Constructor for class org.intermine.web.struts.SaveFromIdsToBagAction
-
- saveHistory(SavedQuery) - Method in class org.intermine.api.profile.Profile
-
Save a query to the query history.
- saveIndexToDatabase(ObjectStore, Map<String, List<FieldDescriptor>>) - Static method in class org.intermine.api.lucene.KeywordSearch
-
writes index and associated directory to the database using the metadatamanager.
- saveKeyDefinitions(String, File, String) - Static method in class org.intermine.modelproduction.MetadataManager
-
Save the key definitions, in serialized form, to the specified directory
- saveModel(Model, File) - Static method in class org.intermine.modelproduction.MetadataManager
-
Save a model, in serialized form, to the specified directory
- saveObjectIdOnTableRow(Integer, Object) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable
-
Set InterMine Object id for the table row
- saveObjectIdOnTableRow(Integer, Object) - Method in class org.intermine.web.logic.results.InlineResultsTable
-
Used on BagUploadConfirm
- savePopulation - Variable in class org.intermine.webservice.server.widget.WidgetsServiceInput
-
- saveProfile(Profile) - Method in class org.intermine.api.profile.ProfileManager
-
Synchronise a user's Profile with the backing store
- saveProperties(String, File, String) - Static method in class org.intermine.modelproduction.MetadataManager
-
Save the objectstore summary, in serialized form, to the specified directory
- saveQueries(Map<? extends String, ? extends PathQuery>) - Method in class org.intermine.api.profile.Profile
-
Save the map of queries as given to the user's profile, avoiding all possible name
collisions.
- saveQueries(Map<String, PathQuery>) - Method in class org.intermine.webservice.server.query.QueryUpdateService
-
- saveQueries(Map<String, PathQuery>) - Method in class org.intermine.webservice.server.query.QueryUploadService
-
Save the given queries.
- saveQuery(String, SavedQuery) - Method in class org.intermine.api.profile.Profile
-
Save or update a query.
- saveQuery(HttpSession, String, PathQuery, Date) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Save a clone of a query to the user's Profile.
- saveQuery(HttpSession, String, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Save a clone of a query to the user's Profile.
- SaveQueryAction - Class in org.intermine.web.struts
-
Implementation of Action that saves a Query from a session.
- SaveQueryAction() - Constructor for class org.intermine.web.struts.SaveQueryAction
-
- SaveQueryForm - Class in org.intermine.web.struts
-
Form bean to represent the inputs to the query saving action
- SaveQueryForm() - Constructor for class org.intermine.web.struts.SaveQueryForm
-
- saveQueryToHistory(HttpSession, String, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Save a clone of a query to the user's Profile history.
- saveTemplate(String, ApiTemplate) - Method in class org.intermine.api.profile.Profile
-
Save a template
- saveToggleState(String, boolean) - Static method in class org.intermine.dwr.AjaxServices
-
Saves information, that some element was toggled - displayed or hidden.
- saveWithBagValues(Integer, Collection<BagValue>) - Method in class org.intermine.api.profile.StorableBag
-
Save the bag into the userprofile database, along with information about what kinds of values
this bag contains.
- savingDisabled - Variable in class org.intermine.api.profile.Profile
-
- SAXParser - Class in org.intermine.util
-
Basic SAX Parser
- sb - Variable in class org.intermine.sql.logging.DatabaseWriter
-
- SC_BAD_REQUEST - Static variable in class org.intermine.webservice.server.output.Output
-
Bad request http status code.
- SC_FORBIDDEN - Static variable in class org.intermine.webservice.server.output.Output
-
Forbidden http status code.
- SC_INTERNAL_SERVER_ERROR - Static variable in class org.intermine.webservice.server.output.Output
-
Internal server http status code.
- SC_NO_CONTENT - Static variable in class org.intermine.webservice.server.output.Output
-
No content http status code.
- SC_NOT_FOUND - Static variable in class org.intermine.webservice.server.output.Output
-
Resource not found http status code.
- SC_OK - Static variable in class org.intermine.webservice.server.output.Output
-
OK http status code.
- SC_UNAUTHORIZED - Static variable in class org.intermine.webservice.server.output.Output
-
Request is legal, but requires authentication, which was
either not provided, or failed.
- schema - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- schema - Variable in class org.intermine.objectstore.intermine.TorqueModelOutput
-
- schema - Variable in class org.intermine.objectstore.intermine.TorqueModelOutputTask
-
- schemaFile - Variable in class org.intermine.task.BuildDbTask
-
- SchemaListService - Class in org.intermine.webservice.server
-
Serve up the list of schemata that we have.
- SchemaListService(InterMineAPI) - Constructor for class org.intermine.webservice.server.SchemaListService
-
Constructor
- SchemaServlet - Class in org.intermine.webservice.server
-
Returns a requested schema.
- SchemaServlet() - Constructor for class org.intermine.webservice.server.SchemaServlet
-
- Scope - Class in org.intermine.api.search
-
Scope constants.
- SCOPES - Static variable in class org.intermine.api.search.Scope
-
The possible scopes.
- score(int) - Method in class org.intermine.sql.precompute.OptimiserCacheLine
-
Scores this cache line according to how far away the required limit is from the limit used to
create the line.
- search(String, Collection<String>, String, boolean, boolean) - Method in class org.intermine.api.bag.BagQueryRunner
-
Given an input list of string identifiers search for corresponding objects.
- SEARCH_INDEX - Static variable in class org.intermine.modelproduction.MetadataManager
-
The name of the key to use to store the search index.
- SEARCH_INDEX_DIRECTORY - Static variable in class org.intermine.modelproduction.MetadataManager
-
The name of the key to use to store the search Directory.
- SEARCH_TRACKER - Static variable in class org.intermine.api.tracker.util.TrackerUtil
-
name of class that tracks searches
- SEARCH_TRACKER_TABLE - Static variable in class org.intermine.api.tracker.util.TrackerUtil
-
name of table that tracks searches
- SearchFilterEngine - Class in org.intermine.api.search
-
Class filtering web searchables according to the associated tags.
- SearchFilterEngine() - Constructor for class org.intermine.api.search.SearchFilterEngine
-
- searchForBag(String, List<String>, String, boolean) - Method in class org.intermine.api.bag.BagQueryRunner
-
Given an input list of string identifiers search for corresponding objects.
- searchItems - Variable in class org.intermine.api.search.SearchRepository
-
- SearchRepository - Class in org.intermine.api.search
-
The base class for search repositories.
- SearchRepository(Profile) - Constructor for class org.intermine.api.search.SearchRepository
-
Constructor.
- SearchResult - Class in org.intermine.api.search
-
A single item in a set or returned results formed by searching the web-searchable indices with
Lucene.
- SearchResults - Class in org.intermine.api.search
-
Representations of Lucene search results over the web-searchable data of the user-profile and
the mechanisms for generating a set of such results.
- SearchTarget - Class in org.intermine.api.search
-
An object for encapsulating the scope and type of object requested from a Lucene search
of the user profile web searchable items.
- SearchTarget(String, String) - Constructor for class org.intermine.api.search.SearchTarget
-
Constructor.
- SEARCHTRACK - Static variable in class org.intermine.api.tracker.xml.SearchTrackBinding
-
label for XML
- SearchTrackBinding - Class in org.intermine.api.tracker.xml
-
- SEARCHTRACKS - Static variable in class org.intermine.api.tracker.xml.SearchTrackBinding
-
label for XML
- SearchUtils - Class in org.intermine.web.search
-
The bits of the search infrastructure that belong in the web-package because
they have view dependent logic.
- seenBrokenOneToMany - Variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
- select - Variable in class org.intermine.sql.query.Query
-
- select(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.TreeAction
-
Process the specified HTTP request, and create the corresponding HTTP
response (or forward to another web component that will create it).
- selectable - Variable in class org.intermine.api.results.Column
-
- selectAll(int, String) - Static method in class org.intermine.dwr.AjaxServices
-
Select all the elements in a PagedTable
- selected - Variable in class org.intermine.web.struts.ModifyTemplateForm
-
- selectedBags - Variable in class org.intermine.web.struts.ModifyBagForm
-
- selectedElements - Variable in class org.intermine.web.struts.ModifyBagDetailsForm
-
- selectedIdsIterator() - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Return an Iterator over the selected Ids
- selectedObjects - Variable in class org.intermine.web.struts.SaveBagForm
-
- selectedQueries - Variable in class org.intermine.web.struts.ModifyQueryForm
-
- selectEncoding(ServletRequest) - Method in class org.intermine.web.filters.SetCharacterEncodingFilter
-
Select an appropriate character encoding to be used, based on the
characteristics of the current request and/or filter initialization
parameters.
- selectId(String, String, String) - Static method in class org.intermine.dwr.AjaxServices
-
Add an ID to the PagedTable selection
- selectId(Integer, int) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Add an object id and its field value
that has been selected in the table.
- SelectValue - Class in org.intermine.sql.query
-
Represents an AbstractValue with an alias, suitable for use in the SELECT portion of an SQL
query.
- SelectValue(AbstractValue, String) - Constructor for class org.intermine.sql.query.SelectValue
-
Construct a new SelectValue.
- sendFareWell(String, String) - Method in class org.intermine.util.Emailer
-
Bid a user farewell from the system.
- SensibleByteArrayOutputStream - Class in org.intermine.util
-
A subclass of ByteArrayOutputStream that behaves a little more sensibly when handling large
writes followed by small writes.
- SensibleByteArrayOutputStream() - Constructor for class org.intermine.util.SensibleByteArrayOutputStream
-
- SensibleByteArrayOutputStream(int) - Constructor for class org.intermine.util.SensibleByteArrayOutputStream
-
- SEPARATOR - Static variable in class org.intermine.api.tag.TagNames
-
Tag separator.
- seqClsName - Variable in class org.intermine.bio.task.GFF3ConverterTask
-
- seqDataSourceName - Variable in class org.intermine.bio.task.GFF3ConverterTask
-
- sequence - Variable in class org.intermine.objectstore.query.ResultsBatches
-
- SEQUENCE_IGNORE - Static variable in interface org.intermine.objectstore.ObjectStore
-
Object representing no fail-fast concurrency checks required.
- SEQUENCE_MULTIPLE - Static variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- sequenceBase - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- sequenceKeys - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
- sequenceNumber - Variable in class org.intermine.objectstore.ObjectStoreAbstractImpl
-
- sequenceOffset - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- SequenceOntology - Class in org.intermine.bio.ontology
-
Helper class for SequenceOntology.
- SequenceOntology(String, InputStream) - Constructor for class org.intermine.bio.ontology.SequenceOntology
-
Constructor.
- SequenceOntologyFactory - Class in org.intermine.bio.ontology
-
Class in charge of making sequence ontology objects
- SequenceProcessor - Class in org.intermine.bio.dataconversion
-
A processor for the chado sequence module.
- SequenceProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.SequenceProcessor
-
Create a new SequenceProcessor
- SequenceService - Class in org.intermine.webservice.server.clob
-
A service to provide access to substrings of ClobAccess data.
- SequenceService(InterMineAPI) - Constructor for class org.intermine.webservice.server.clob.SequenceService
-
- sequential - Variable in class org.intermine.objectstore.query.Results
-
- SERIAL_NUMBER - Static variable in class org.intermine.modelproduction.MetadataManager
-
The name of the key used to store the serial number identifying the production db
- SERIAL_SEQUENCE_NAME - Static variable in class org.intermine.task.BuildDbTask
-
- serialize(Properties) - Static method in class org.intermine.util.PropertiesUtil
-
Serialize properties to a string suitable for a subsequent load()
- serveToken(DeletionToken) - Method in class org.intermine.webservice.server.user.NewDeletionTokenService
-
Serve a token to the outside world.
- Service - Class in org.intermine.webservice.client.core
-
This class provides the base level common functionality required to access
any InterMine service.
- Service(String, String, String) - Constructor for class org.intermine.webservice.client.core.Service
-
Constructor.
- service(HttpServletRequest, HttpServletResponse) - Method in class org.intermine.webservice.server.WebService
-
Starting method of web service.
- SERVICE_FAILED_MSG - Static variable in class org.intermine.webservice.server.WebServiceConstants
-
Error message returned in case of unexpected service failure.
- serviced - Static variable in class org.intermine.objectstore.query.PrefetchManager
-
Set of requests currently being serviced.
- ServiceException - Exception in org.intermine.webservice.client.exceptions
-
ServiceException is a base class for all service exceptions.
- ServiceException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceException
-
- ServiceException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceException
-
- ServiceException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceException
-
- ServiceException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceException
-
Exception is filled in with some detailed information from response.
- ServiceException - Exception in org.intermine.webservice.server.exceptions
-
ServiceException is a base class for all service exceptions.
- ServiceException(String) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
-
- ServiceException(String, int) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
-
- ServiceException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
-
- ServiceException(String, Throwable, int) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
-
- ServiceException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
-
- ServiceException(Throwable, int) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceException
-
- ServiceFactory - Class in org.intermine.webservice.client.core
-
The Class that should be used for creating services.
- ServiceFactory(String) - Constructor for class org.intermine.webservice.client.core.ServiceFactory
-
Construct a service factory with a default application name.
- ServiceFactory(String, String) - Constructor for class org.intermine.webservice.client.core.ServiceFactory
-
Construct a factory for gaining access to specific resources.
- ServiceFactory(String, String, String) - Constructor for class org.intermine.webservice.client.core.ServiceFactory
-
Deprecated.
This method causes username and password information to be insecurely
transmitted over HTTP connections. Use the token authentication mechanism instead.
- ServiceForbiddenException - Exception in org.intermine.webservice.client.exceptions
-
The ServiceForbiddenException is thrown by a service when an
attempt is made to service that is disabled.
- ServiceForbiddenException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceForbiddenException
-
- ServiceForbiddenException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceForbiddenException
-
- ServiceForbiddenException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceForbiddenException
-
- ServiceForbiddenException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceForbiddenException
-
- ServiceForbiddenException - Exception in org.intermine.webservice.server.exceptions
-
The ServiceForbiddenException is thrown by a service when an attempt is made to service that
is disabled.
- ServiceForbiddenException(String) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceForbiddenException
-
- ServiceForbiddenException(String, Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceForbiddenException
-
- ServiceForbiddenException(Throwable) - Constructor for exception org.intermine.webservice.server.exceptions.ServiceForbiddenException
-
- ServiceListingHandler - Class in org.intermine.webservice.server
-
- ServiceListingHandler() - Constructor for class org.intermine.webservice.server.ServiceListingHandler
-
- ServicesListingsServlet - Class in org.intermine.webservice.server
-
Provide a list of all the services available at this mine.
- ServicesListingsServlet() - Constructor for class org.intermine.webservice.server.ServicesListingsServlet
-
- serviceThreads - Static variable in class org.intermine.objectstore.query.PrefetchManager
-
- ServiceUnavailableException - Exception in org.intermine.webservice.client.exceptions
-
The ServiceUnavailableException is thrown when an exception occurs that
is temporary, the user should try it again.
- ServiceUnavailableException(String) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceUnavailableException
-
- ServiceUnavailableException(String, Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceUnavailableException
-
- ServiceUnavailableException(Throwable) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceUnavailableException
-
- ServiceUnavailableException(HttpConnection) - Constructor for exception org.intermine.webservice.client.exceptions.ServiceUnavailableException
-
- SessionActivationListener - Class in org.intermine.web.logic.session
-
Added to each session to monitor activation events.
- SessionActivationListener() - Constructor for class org.intermine.web.logic.session.SessionActivationListener
-
- sessionCreated(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionListener
- sessionDestroyed(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionListener
- sessionDidActivate(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionActivationListener
-
Called after a session is unserialised.
- sessionIdentifier - Variable in class org.intermine.api.tracker.track.TrackAbstract
-
- SessionlessRequest - Class in org.intermine.webservice.server.core
-
- SessionlessRequest(HttpServletRequest) - Constructor for class org.intermine.webservice.server.core.SessionlessRequest
-
Construct a request by wrapping the given request.
- SessionListener - Class in org.intermine.web.logic.session
-
Perform InterMine-specific actions when a Session is constructed or destroyed
- SessionListener() - Constructor for class org.intermine.web.logic.session.SessionListener
-
- SessionMethods - Class in org.intermine.web.logic.session
-
Business logic that interacts with session data.
- SessionService - Class in org.intermine.webservice.server
-
Open a new 24-hour session.
- SessionService(InterMineAPI) - Constructor for class org.intermine.webservice.server.SessionService
-
- sessionWillPassivate(HttpSessionEvent) - Method in class org.intermine.web.logic.session.SessionActivationListener
-
Called just before serialising to disk.
- set(int, boolean) - Method in class org.intermine.util.IntPresentSet
-
Adds the given int to the set.
- set(int, Object) - Method in class org.intermine.webservice.client.results.ResultRowList
-
- setAccepted(Boolean) - Method in class org.intermine.api.bag.SharingInvite
-
- setAccessions(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setAction(String) - Method in class org.intermine.web.struts.WidgetForm
-
- setActionType(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
-
- setAdditionsFile(File) - Method in class org.intermine.task.ModelMergerTask
-
The file containing model additions.
- setAdditionsFiles(List<File>) - Method in class org.intermine.task.ModelMergerTask
-
The files containing model additions.
- setAlias(String) - Method in class org.intermine.sql.query.AbstractTable
-
Sets the alias for this AbstractTable object.
- setAlias(String) - Method in class org.intermine.task.CreateIndexesTask
-
Set the ObjectStore alias.
- setAlias(String) - Method in class org.intermine.task.DropPrecomputedTablesTask
-
Set the ObjectStore alias
- setAlias(String) - Method in class org.intermine.task.PrecomputeTask
-
Set the ObjectStore alias.
- setAlias(String) - Method in class org.intermine.task.RunIqlQueryTask
-
Set the ObjectStore alias.
- setAlias(String) - Method in class org.intermine.task.SummariseObjectStoreTask
-
Set the ObjectStore alias
- setAlias(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
-
Set the ObjectStore alias
- setAllowduplicates(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
-
Toggle whether or not to allow duplicate sequences
- setAllSelectedColumn(int) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Select a whole column.
- setAllSources(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
-
Set the list of data sources present in the project.xml, for the purposes of verifying the
priorities properties file.
- setAPI(InterMineAPI) - Method in class org.intermine.api.template.ApiTemplate
-
Only used on export so we can get the tags related to this template.
- setApiKey(String) - Method in class org.intermine.api.profile.Profile
-
Set the API token for this user, and save it in the backing DB.
- setAppendConfig(Boolean) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
-
Set whether to append config from parent
- setApplicationName(String) - Method in class org.intermine.webservice.client.core.ServiceFactory
-
Set the application name used to identify your requests to the server
- setAspectDisplayers(Map<String, List<Displayer>>) - Method in class org.intermine.web.logic.config.Type
-
- setAspects(String) - Method in class org.intermine.web.logic.config.Displayer
-
Set the aspects of this displayer
- setAspects(ServletContext, Map<String, Aspect>) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Sets the Map of aspects.
- setAttribute(Integer, String, String) - Method in class org.intermine.bio.dataconversion.ChadoProcessor
-
Set an attribute in an Item by creating an Attribute object and storing it.
- setAttribute(String, Object) - Static method in class org.intermine.web.context.InterMineContext
-
Set an attribute of the context.
- setAttribute(String, String) - Method in class org.intermine.xml.full.Item
-
Add an attribute to this item.
- setAttributeIndexes(boolean) - Method in class org.intermine.task.CreateIndexesTask
-
Set the attributeIndexes flag.
- setAttributeOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Sets the value of attributeOp
- setAttributeOps(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm
-
Set the attribute ops
- setAttributeOps(String, String) - Method in class org.intermine.web.struts.TemplateForm
-
Set an attribute op
- setAttributeOptions(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Sets the value of attributeOptions
- setAttributeToEmptyString(String) - Method in class org.intermine.xml.full.Item
-
Add an attribute to this item and set it to the empty string.
- setAttributeValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Sets the value of attributeValue
- setAttributeValues(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm
-
Set the attribute values
- setAttributeValues(String, Object) - Method in class org.intermine.web.struts.TemplateForm
-
Set an attribute value
- setAuthentication(String, String) - Method in class org.intermine.webservice.client.core.Service
-
Deprecated.
Use token based authentication instead (Service.setAuthentication(String)
as this method will cause your user name and password to be transmitted
insecurely across HTTP connections.
- setAuthentication(String) - Method in class org.intermine.webservice.client.core.Service
-
Set the token to be used for authentication.
- setAuthToken(String) - Method in interface org.intermine.webservice.client.core.Request
-
Set the authentication token for the request
- setAuthToken(String) - Method in class org.intermine.webservice.client.core.RequestImpl
-
- setAutoCompleter(ServletContext, AutoCompleter) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Set the AutoCompleter into the ServletContext.
- setBag(InterMineBag) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setBag(String, Object) - Method in class org.intermine.web.struts.TemplateForm
-
Set the bag name.
- setBagName(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
name of bag that this widget is using.
- setBagName(String) - Method in class org.intermine.web.struts.FindInListForm
-
- setBagName(String) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
-
Set the value of bagName
- setBagName(String) - Method in class org.intermine.web.struts.WidgetForm
-
name of bag that this widget is using.
- setBagOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Sets the value of bagOp
- setBagOp(String, String) - Method in class org.intermine.web.struts.TemplateForm
-
Set bag operation.
- setBagSelected(boolean) - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Set if the bag is selected, used by the method isBagSelected that returns true,
even if the constraint is an attribute constraint
- setBagTableNames(Map<Object, String>) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- setBagType(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- setBagType(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm
-
Set the bag type
- setBagType(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setBagType(String) - Method in class org.intermine.web.struts.WidgetForm
-
- setBagValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Sets the value of bagValue
- setBaseLink(String) - Method in class org.intermine.web.tags.table.NavigationBarTag
-
- setBatchSize(int) - Method in class org.intermine.api.query.PathQueryExecutor
-
Sets batch size.
- setBatchSize(int) - Method in interface org.intermine.objectstore.proxy.LazyCollection
-
Sets the number of rows requested from the ObjectStore whenever an execute call is made
- setBatchSize(int) - Method in class org.intermine.objectstore.proxy.ProxyCollection
-
Sets the number of rows requested from the ObjectStore whenever an execute call is made
- setBatchSize(int) - Method in class org.intermine.objectstore.query.Results
-
Sets the number of rows requested from the ObjectStore whenever an execute call is made
- setBatchSize(int) - Method in class org.intermine.objectstore.query.ResultsBatches
-
Sets the number of rows requested from the ObjectStore whenever an execute call is made
- setBatchWriter(BatchWriter) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Allows the changing of the BatchWriter that this ObjectStoreWriter uses.
- setBatchWriter(BatchWriter) - Method in class org.intermine.sql.writebatch.Batch
-
Changes the BatchWriter for a new one.
- setBiogridOrganisms(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter
-
Sets the list of taxonIds that should be imported if using split input files.
- setBlockCount(int) - Method in class org.intermine.bio.io.bed.BEDRecord
-
- setBlockCount(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- setBlockSizes(List<Integer>) - Method in class org.intermine.bio.io.bed.BEDRecord
-
- setBlockSizes(List<Integer>) - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- setBlockStarts(List<Integer>) - Method in class org.intermine.bio.io.bed.BEDRecord
-
- setBlockStarts(List<Integer>) - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- setBuildDir(String) - Method in class org.intermine.web.task.IssueTokenTask
-
Bean-style setter, as per the ant spec.
- setCacheDirName(String) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
-
Set the cache file name
- setCaseSensitive(boolean) - Method in class org.intermine.web.struts.BuildBagForm
-
- setCategories(ServletContext, Set<String>) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Sets the aspect categories into the servlet context.
- setCategoryPath(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- SetCharacterEncodingFilter - Class in org.intermine.web.filters
-
Example filter that sets the character encoding to be used in parsing the
incoming request, either unconditionally or only if the client did not
specify a character encoding.
- SetCharacterEncodingFilter() - Constructor for class org.intermine.web.filters.SetCharacterEncodingFilter
-
- setCharSet(String) - Method in class org.intermine.webservice.client.core.ContentType
-
Sets character set of this content type.
- setChildTermId(String) - Method in class org.intermine.bio.ontology.OboRelation
-
- setChrom(String) - Method in class org.intermine.bio.io.bed.BEDRecord
-
- setChrom(String) - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- setChromEnd(int) - Method in class org.intermine.bio.io.bed.BEDRecord
-
- setChromEnd(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- setChromosomeLocationsAndLengths() - Method in class org.intermine.bio.postprocess.CalculateLocations
-
For each SequenceFeature, if it has a Location on a Chromosome, set the
SequenceFeature.chromosomeLocation reference to be that Location and set the length
field of the SequenceFeature to chromosomeLocation.end - chromosomeLocation.start + 1
- setChromStart(int) - Method in class org.intermine.bio.io.bed.BEDRecord
-
- setChromStart(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- setClassAttribute(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
The attribute of the class created to set with the identifying field.
- setClassConfig(Type) - Method in class org.intermine.web.logic.config.FieldConfig
-
- setClassDescriptor(String) - Method in class org.intermine.xml.full.Item
-
Set the classDescriptor attribute to be the ClassDescriptor for the given className in the
Model set by setModel().
- setClassKeys(Map<String, List<FieldDescriptor>>) - Method in class org.intermine.api.bag.operations.BagOperation
-
- setClassKeys(Map<String, List<FieldDescriptor>>) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
- setClassLoader(ClassLoader) - Method in class org.intermine.web.task.CreateSearchIndexTask
-
Set the class loader
- setClassName(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
The class name to use for objects created during load.
- setClassName(String) - Method in class org.intermine.task.AnalyseDbTask
-
Set an optional class name, must also set model name
- setClassName(String) - Method in class org.intermine.task.StaticMethodTask
-
Set class name on which to call static method.
- setClassName(String) - Method in class org.intermine.web.logic.config.TableExportConfig
-
Set the className of this TableExportConfig
- setClassName(String) - Method in class org.intermine.web.logic.config.Type
-
Set the unqualified class name for this Type (from fully-qualified)
- setClassName(String) - Method in class org.intermine.web.logic.results.InlineResultsTableRow
-
- setClassName(String) - Method in class org.intermine.web.struts.QueryClassSelectForm
-
Set the class name
- setClassName(String) - Method in class org.intermine.xml.full.Item
-
Set the class of this item.
- setClassNameOnTableRow(String, Object) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTable
-
Set a class name on table row
- setClassNameOnTableRow(String, Object) - Method in class org.intermine.web.logic.results.InlineResultsTable
-
Set a class name on table row, used for type safety as overriden on BagUploadConfirm
- setClsName(String) - Method in class org.intermine.task.DBConverterTask
-
Set the source specific subclass of FileConverter to run
- setClsName(String) - Method in class org.intermine.task.DirectoryConverterTask
-
Set the source specific subclass of DirectoryConverter to run
- setClsName(String) - Method in class org.intermine.task.FileConverterTask
-
Set the source specific subclass of FileConverter to run
- setClsName(String) - Method in class org.intermine.task.PostProcessorTask
-
Set the name of the PostProcessor sub-class to load to do the postprocessing.
- setCode(String) - Method in class org.intermine.web.logic.query.DisplayConstraint
-
- setCode(String) - Method in class org.intermine.web.logic.template.ConstraintInput
-
- setCollection(String, List<String>) - Method in class org.intermine.xml.full.Item
-
Set a collection.
- setColumnId(String) - Method in class org.intermine.api.results.Column
-
- setColumnNames(List<String>) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Set the column names
- setColumnNames(List<String>) - Method in class org.intermine.web.tags.table.TableTag
-
- setColumnTitle(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
- setComment(String) - Method in class org.intermine.template.TemplateQuery
-
Set the private comment for this template.
- setComment(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
-
Set the comment
- setCommentEvidence(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setComments(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setCommentType(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
Creates a new temporary object to hold the type and later the publications for this comment.
- setComplete(long) - Method in class org.intermine.objectstore.query.ResultsInfo
-
Sets the estimated amount of time taken to produce the entire set of results.
- setComputeTotalCount(boolean) - Method in class org.intermine.webservice.server.query.result.QueryResultInput
-
Sets true if compute total count of all available results.
- setConfigFile(File) - Method in class org.intermine.task.AcceptanceTestTask
-
Set the File to read configuration from
- setConfigFileName(String) - Method in class org.intermine.task.SummariseObjectStoreTask
-
Set the name of the Properties file containing the names of the classes and fields to
summarise.
- setConfigurationFile(File) - Method in class org.intermine.task.TSVFileReaderTask
-
Set the configuration file to use.
- setConnectField(String) - Method in class org.intermine.api.bag.BagQueryConfig
-
Set the connecting field for adding an extra constraint to bag queries.
- setConnectionTimeout(int) - Method in class org.intermine.webservice.client.core.Service
-
Sets connection timeout.
- setConstrainField(String) - Method in class org.intermine.api.bag.BagQueryConfig
-
Set the field to constrain when making an extra constraint.
- setConstraint(TemplateQuery, TemplateValue) - Static method in class org.intermine.api.template.TemplatePopulator
-
Set the value for a constraint in the template query with the given TemplateValue.
- setConstraint(Constraint) - Method in class org.intermine.objectstore.query.Query
-
Constrain this Query using either a single constraint or a set of constraints
- setConstraint(Constraint) - Method in interface org.intermine.objectstore.query.Queryable
-
Sets the additional constraint.
- setConstraint(Constraint) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
-
Sets the additional constraint.
- setConstraint(Constraint) - Method in class org.intermine.objectstore.query.QueryObjectPathExpression
-
Sets the additional constraint.
- setConstraintDescription(PathConstraint, String) - Method in class org.intermine.template.TemplateQuery
-
Sets the description for a constraint.
- setConstraintLogic(String) - Static method in class org.intermine.dwr.AjaxServices
-
Set the constraint logic on a query to be the given expression.
- setConstraintLogic(String) - Method in class org.intermine.pathquery.PathQuery
-
Sets the current constraint logic.
- setConstraintOp(ConstraintOp) - Method in class org.intermine.web.logic.template.ConstraintInput
-
Sets constraint operation.
- setConstraints(Map<String, List<ConstraintInput>>) - Method in class org.intermine.web.logic.template.TemplateResultInput
-
Sets constraints.
- setConstraints(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- setConstraintsForView(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- setContent(String) - Method in class org.intermine.web.logic.widget.config.HTMLWidgetConfig
-
Set the content of the widget.
- setContent(File) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo
-
Set the content for this creation request as coming from a file on the file-system.
- setContent(InputStream) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo
-
Set the content for this creation request as coming from an InputStream.
- setContent(Collection<String>) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo
-
Set the content for this request as coming from a set of strings, with each
string representing one identifier.
- setContent(String...) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo
-
Set the content for this request as coming from a set of strings, with each
string representing one identifier.
- setContent(String) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo
-
Set the content as coming from a string.
- setContent(PathQuery) - Method in class org.intermine.webservice.client.services.ListService.ListCreationInfo
-
Set the content for this request as a query to run to find objects with.
- setContentType(ContentType) - Method in interface org.intermine.webservice.client.core.Request
-
- setContentType(ContentType) - Method in class org.intermine.webservice.client.core.RequestImpl
- setConverter(GFF3Converter) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
- setConverter(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
-
Set the converter
- setCorrection(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
-
- setCorrectionCoefficient(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- setCount(int) - Method in class org.intermine.web.logic.session.QueryCountQueryMonitor
-
Set the query count/size.
- setCountFormat() - Method in class org.intermine.webservice.client.core.RequestImpl
-
Set the format as count format.
- setCreategenes(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
-
Toggle whether or not to create genes and protein/gene associations.
- setCreatego(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
-
Toggle whether or not to import GO data
- setCreateinterpro(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
-
Deprecated.
The UniProt data source does not create interpro domains any longer. Please
use the InterPro data source instead.
- setCreaterelations(String) - Method in class org.intermine.bio.dataconversion.OboConverter
-
Set to false to prevent storing OntologyRelation objects that include the relationship types
between terms.
- setCSVContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets comma separated values content type.
- setCSVHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets response header and content type for comma separated
values output.
- setCurrentFile(File) - Method in class org.intermine.dataconversion.FileConverter
-
Set the current File that is being processed.
- setCurrentMapFromCurrentArray(ResultElement) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
-
Finds the object we should be dealing with by getting it from the current array.
- setCurrentMapFromCurrentArray() - Method in class org.intermine.webservice.server.output.JSONResultsIterator
-
Sets the current map to work with by getting the last one from the current array.
- setCurrentPage(Integer) - Method in class org.intermine.web.tags.table.NavigationBarTag
-
- setCustomContentType(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets content type to the parameter specified
- setCustomTypeHeader(HttpServletResponse, String, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets response header and content type for a custom content type.
- setDatabase(String) - Method in class org.intermine.task.AcceptanceTestTask
-
Set the database alias
- setDatabase(String) - Method in class org.intermine.task.GrantTask
-
Set the database alias
- setDataDir(String) - Method in class org.intermine.task.DirectoryConverterTask
-
Set the dataDir.
- setDataSet(String) - Method in class org.intermine.bio.dataconversion.BioDirectoryConverter
-
Update the dataset reference Id.
- setDataSet(String) - Method in class org.intermine.bio.dataconversion.BioStoreHook
-
Update the dataset reference Id.
- setDatasetRefId(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setDataSets(Model, Item, String, String) - Static method in class org.intermine.bio.dataconversion.BioStoreHook
-
Do the work of processItem() by setting DataSet and DataSource references and collections
on the given Item.
- setDataSetTitle(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
If a value is specified this title will used when a DataSet is created.
- setDataSetTitle(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
-
Set the dataSetTitle
- setDataSourceName(String) - Method in class org.intermine.bio.dataconversion.BioDBConverter
-
Set the name of the DataSource Item to create for this converter.
- setDataSourceName(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
Datasource for any bioentities created
- setDataSourceName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
-
Set the dataSourceName
- setDate(Date) - Method in class org.intermine.api.profile.InterMineBag
-
Sets date when bag was created.
- setDb(Database) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- setDbAlias(String) - Method in class org.intermine.task.DBConverterTask
-
Set the Database to read from
- setDbrefs(Map<String, Set<String>>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setDefaultValue(String, String) - Method in class org.intermine.webservice.server.widget.WidgetsRequestParser
-
Set a parameter default.
- setDeleteTracks(boolean) - Method in class org.intermine.web.struts.TemplatesImportForm
-
Set the deleteTracks flag.
- setDescr(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setDescription(String) - Method in class org.intermine.api.profile.InterMineBag
-
- setDescription(String) - Method in class org.intermine.api.template.ApiTemplate
-
- setDescription(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
-
- setDescription(String) - Method in class org.intermine.bio.ontology.OboTerm
-
Set the term description.
- setDescription(String, String) - Method in class org.intermine.pathquery.PathQuery
-
Sets the description for a given path.
- setDescription(String) - Method in class org.intermine.pathquery.PathQuery
-
Sets the description for this PathQuery.
- setDescription(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- setDescription(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
-
Set the description
- setDescriptor(FieldDescriptor) - Method in class org.intermine.web.logic.results.InlineList
-
Set FieldDescriptor so we can work with placements
- setDestDir(File) - Method in class org.intermine.task.ModelOutputTask
-
Sets the directory that output should be written to.
- setDestDir(File) - Method in class org.intermine.task.RetrieveMetadataTask
-
Sets the destination directory
- setDestFile(File) - Method in class org.intermine.objectstore.intermine.TorqueModelOutputTask
-
Sets the file to which the data should be written.
- setDirect(boolean) - Method in class org.intermine.bio.ontology.OboRelation
-
- setDirectChildren(Set<ChadoCVTerm>) - Method in class org.intermine.bio.chado.ChadoCVTerm
-
Set the direct children of this term.
- setDirectParents(Set<ChadoCVTerm>) - Method in class org.intermine.bio.chado.ChadoCVTerm
-
Set the direct parents of this term.
- setDisableResultsCache(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Sets the disableResultsCache configuration option.
- setDisableResultsCache(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Sets the disableResultsCache configuration option.
- setDisease(String, String) - Method in class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder
-
- setDisplayer(String) - Method in class org.intermine.web.logic.config.FieldConfig
-
Set the displayer
- setDisplayFields(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
- setDistinct(boolean) - Method in class org.intermine.objectstore.query.Query
-
Set the value of the distinct property, which determines whether duplicates are
permitted in the results returned by this Query
- setDistinct(boolean) - Method in class org.intermine.sql.query.Query
-
Sets the distinct status of this query.
- setDoGzip(boolean) - Method in class org.intermine.web.struts.TableExportForm
-
Set whether the output should be GZIPped.
- setDomain(String) - Method in class org.intermine.api.beans.PartnerLink
-
- setDomainLabel(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
Set the value of domainLabel
- setDomains(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setDoNotTruncate(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
-
If set to true, don't truncate long fields or put in a [View all...] link in the object
details page.
- setDontCreateLocations(boolean) - Method in class org.intermine.bio.dataconversion.GFF3Converter
-
Set the dontCreateLocations flag
- setDontCreateLocations(boolean) - Method in class org.intermine.bio.task.GFF3ConverterTask
-
Set the dontCreateLocations flag, the default is false - create locations.
- setDuplicate(boolean) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setEditable(PathConstraint, boolean) - Method in class org.intermine.template.TemplateQuery
-
Sets a constraint to be editable or not.
- seteditable(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- setEditable(boolean) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Set the editable flag (when building a template).
- setEditableConstraints(List<PathConstraint>) - Method in class org.intermine.template.TemplateQuery
-
Sets the list of editable constraints to exactly that provided, in the given order.
- setEditableInTemplate(boolean) - Method in class org.intermine.web.logic.query.DisplayConstraint
-
- setEdited(boolean) - Method in class org.intermine.template.TemplateQuery
-
Set the query as being edited.
- setEditingConstraintCode(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Set the code of an existing constraint that is being edited.
- setEmail(String) - Method in class org.intermine.web.task.IssueTokenTask
-
Bean-style setter, as per the ant spec.
- setEnd(int) - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
-
Set end value
- setEnrich(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- setEnrichIdentifier(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- setEnsemblDb(String) - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask
-
Sets the value of ensemblDb
- setEnsemblPrefix(String) - Method in class org.intermine.bio.util.OrganismData
-
- setEof(HintingFetcher) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Sets the equivalent object fetcher.
- setErr(OutputStream) - Method in class org.intermine.web.task.KeyStoreTask
-
Set the error handler
- setError(String, int) - Method in class org.intermine.webservice.server.output.Output
-
Sets the error message
- setErrorCorrection(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setErrorCorrection(String) - Method in class org.intermine.web.struts.WidgetForm
-
- setErrorOnInitialiser(ServletContext, Map<String, String>) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Sets the blocking error codes into the servlet context.
- setEscapeXml(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
-
If set to true, don't escape the field value on object
details page.
- setEstimatedRows(long) - Method in class org.intermine.sql.query.ExplainResult
-
Use this to provide the object with a "better" estimate of the number of rows in the results
of this Query.
- setExcludeList(String) - Method in class org.intermine.task.ConverterTask
-
Sets the list of classes to NOT try and convert
- setExistingBagName(String) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
-
Sets the value of existingBagName
- setExistingBagName(String) - Method in class org.intermine.web.struts.SaveBagForm
-
Sets the value of existingBagName
- setExpiry(String) - Method in class org.intermine.web.task.IssueTokenTask
-
Bean-style setter, as per the ant spec.
- setExplain(boolean) - Method in class org.intermine.sql.query.Query
-
Sets the explain status of this query.
- setExportField(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
- setExporttype(String) - Method in class org.intermine.web.struts.WidgetForm
-
- setExternalLink(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- setExternalLink(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
- setExternalLink(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setExternalLinkLabel(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
- setExtraAttribute(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
-
- setExtraConstraintClassName(String) - Method in class org.intermine.api.bag.BagQueryConfig
-
Set the class name of extra constraint to use in BagQuery objects using this config object.
- setExtraFieldValue(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm
-
Set the extra field value
- setExtraFieldValue(String) - Method in class org.intermine.web.struts.BuildBagForm
-
Set the extra field value.
- setExtraFieldValue(String) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
-
- setExtraThreads(int) - Method in class org.intermine.task.CreateIndexesTask
-
Set the number of extra worker threads.
- setExtraValue(String) - Method in class org.intermine.web.logic.template.ConstraintInput
-
Sets extra value
- setExtraValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Sets the value of extraValue
- setExtraValue(String) - Method in class org.intermine.webservice.server.lists.ListsServiceInput
-
An extra value, such as an organism, for use in lookup constraints.
- setExtraValues(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm
-
Sets the extra values
- setExtraValues(String, Object) - Method in class org.intermine.web.struts.TemplateForm
-
Set an extra value
- setFactory(ServiceFactory) - Method in class org.intermine.webservice.client.core.Service
-
Set the ServiceFactory this service can use to access other services.
- setFastaTaxonId(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
Set the Taxon Id of the Organism we are loading.
- setFavourite(String, String, boolean) - Method in class org.intermine.dwr.AjaxServices
-
Creates a favourite Tag for the given templateName
- setFeature(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Set the feature item for this record.
- setFetchFields(boolean, Set<FieldDescriptor>) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsImpl
-
Sets variables which determines which fields are prefetched.
- setField(Object) - Method in class org.intermine.api.results.ResultElement
-
Set the field value
- SetFieldConfigAction - Class in org.intermine.bio.chado.config
-
An action that sets an attribute in a new Item.
- SetFieldConfigAction(String) - Constructor for class org.intermine.bio.chado.config.SetFieldConfigAction
-
Create a new SetFieldConfigAction that sets the given field.
- SetFieldConfigAction(String, Pattern) - Constructor for class org.intermine.bio.chado.config.SetFieldConfigAction
-
Create a new SetFieldConfigAction that sets the given field.
- setFieldExporter(String) - Method in class org.intermine.web.logic.config.FieldConfig
-
Set the class name of the FieldExporter to use when this field is viewed.
- setFieldExpr(String) - Method in class org.intermine.web.logic.config.FieldConfig
-
Set the JSTL expression for this field which will be evaluated in the request context when
the JSP is viewed.
- setFieldToAlias(FromElement, Map<String, String>) - Method in class org.intermine.objectstore.intermine.SqlGenerator.State
-
- setFieldValue(String, Object) - Method in class org.intermine.objectstore.proxy.ProxyReference
- setFieldValue(Object, String, Object) - Static method in class org.intermine.util.DynamicUtil
-
Sets the value of a public or protected Field of an Object given the field name.
- setFile(String) - Method in class org.intermine.bio.task.OboConverterTask
-
Set the input file name
- setFile(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
-
Set a file name to load from
- setFile(String) - Method in class org.intermine.task.FullXmlConverterTask
-
Set a file name to load from
- setFileArray(File[]) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
Directly set the array of files to read from.
- setFileName(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets the content disposition filename.
- setFileName(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
-
Set the name of the file to write to.
- setFileName(String) - Method in class org.intermine.web.task.ProfileReadTask
-
Set the name of the file to read from.
- setFileName(String) - Method in class org.intermine.web.task.ProfileWriteTask
-
Set the name of the file to write to.
- setFileName(String) - Method in class org.intermine.web.task.TemplateTrackReadTask
-
Set the name of the file to read from.
- setFileName(String) - Method in class org.intermine.web.task.TemplateTrackWriteTask
-
Set the name of the file to write to.
- setFilter(String) - Method in class org.intermine.web.logic.widget.EnrichmentWidget
-
- setFilter(String) - Method in class org.intermine.web.logic.widget.GraphWidget
-
- setFilter(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setFilter(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
-
- setFilterLabel(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- setFilterLabel(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setFilters(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- setFilters(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setFlattenedResults() - Method in class org.intermine.web.logic.widget.TableWidgetLdr
-
builds, runs query.
- setFormat(String) - Method in class org.intermine.web.struts.CSVExportForm
-
Set the format.
- setFormat(String) - Method in class org.intermine.webservice.client.core.RequestImpl
-
Set the format for the request.
- setFormat(Format) - Method in class org.intermine.webservice.server.WebService
-
For very picky services, you can just set it yourself, and say "s****w you requester".
- setFormFile(FormFile) - Method in class org.intermine.web.struts.BuildBagForm
-
Set the FormFile.
- setFormFile(FormFile) - Method in class org.intermine.web.struts.ImportXMLForm
-
Set the FormFile.
- setFragment(boolean) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
dev can configure converter to load these or not.
- setFull(boolean) - Method in class org.intermine.task.AnalyseDbTask
-
Set true if a VACUUM FULL ANALYSE required
- setGaff(String) - Method in class org.intermine.bio.dataconversion.GoConverter
-
Sets the file format for the GAF. 2.0 is the default.
- setGeneDesignation(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
-
set the gene designation for this taxon. can be NULL
- setGeneSource(FeatureData, String) - Method in class org.intermine.bio.dataconversion.ModEncodeFeatureProcessor
-
Method to set the source for gene
for modencode datasources it will add the title
- setGeneSource(Integer, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
to set source field if in the model (modmine)
- setGeneSource(FeatureData, String) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
set the source field for modENCODE gene
- setGlobalSearchRepository(ServletContext, SearchRepository) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Set the SearchRepository for global (public) objects in the servlet context.
- setGOTerms(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setGraphType(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- setGzippedContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets gzip content type ("application/octet-stream")
- setGzippedHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets response header and content type for gzipped output.
- setHandlerClassName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
-
Set the name of GFF3RecordHandler class to use when processing.
- setHeader(String, String) - Method in interface org.intermine.webservice.client.core.Request
-
Sets a request header.
- setHeader(String, String) - Method in class org.intermine.webservice.client.core.RequestImpl
-
Sets a request header.
- setHeaderAttributes(Map<String, Object>) - Method in class org.intermine.webservice.server.output.Output
-
Sets header attributes that are displayed for example in xml header.
- setHeaderAttributes(Map<String, Object>) - Method in class org.intermine.webservice.server.output.StreamedOutput
-
Sets header attributes that are displayed for example in xml header.
- setHeaderAttributes(String) - Method in class org.intermine.webservice.server.query.QueryToListService
-
Sets the header attributes map on the current output object.
- setHeaderAttributes(PathQuery, Integer, Integer) - Method in class org.intermine.webservice.server.query.result.QueryResultService
-
Set the header attributes of the output based on the values of the PathQuery
- setHeaderAttributes(PathQuery, Integer, Integer) - Method in class org.intermine.webservice.server.query.result.TableRowService
-
- setHide(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
-
If set to true, do not display field on report page.
- setHighlight(String) - Method in class org.intermine.web.struts.WidgetForm
-
- setHTMLContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets HTML content type.
- setIconImage(String) - Method in class org.intermine.web.logic.aspects.Aspect
-
Set the icon Image
- setId(String) - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Set the Id of this GFF3Record.
- setId(String) - Method in class org.intermine.bio.ontology.OboTypeDefinition
-
- setId(Integer) - Method in interface org.intermine.model.InterMineObject
-
Setter for the ID field.
- setId(Integer) - Method in class org.intermine.objectstore.proxy.ProxyReference
-
Sets the ID value
- setId(String) - Method in class org.intermine.web.logic.config.TableExportConfig
-
Set the id of this TableExportConfig
- setId(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- setId(String) - Method in class org.intermine.web.tags.disclosure.DisclosureTag
-
Sets element id.
- setIdentifier(String) - Method in class org.intermine.api.beans.ObjectDetails
-
- setIdentifier(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter.DiseaseHolder
-
- setIdentifier(String) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
-
Set identifier
- setIdentifier(String) - Method in class org.intermine.xml.full.Item
-
Set the identifier of this item.
- setIdentifierMap(Map<?, ?>) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Set the Map of GFF identifiers to Item identifier.
- setIdentifierName(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
-
- setIdSuffix(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
Set the suffix to add to identifiers from the FASTA file when creating
BioEnitys.
- setIgnore(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
-
Set a comma separated list of template names to ignore - i.e. not precompute.
- setIgnoreDuplicates(boolean) - Method in interface org.intermine.dataloader.IntegrationWriter
-
Tell this IntegrationWriter whether to ignore duplicate objects from the same source.
- setIgnoreDuplicates(boolean) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Tell this IntegrationWriter whether to ignore duplicate objects from the same source.
- setIgnoreDuplicates(boolean) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
-
Set the value of ignoreDuplicates for the IntegrationWriter.
- setIgnoreDuplicates(boolean) - Method in class org.intermine.dataloader.XmlDataLoaderTask
-
Set the value of ignoreDuplicates for the IntegrationWriter
- setIgnoreDuplicates(boolean) - Method in class org.intermine.task.DirectDataLoaderTask
-
Set the value of ignoreDuplicates for the IntegrationWriter
- setImage(String) - Method in class org.intermine.web.logic.config.HeaderConfigLink
-
Set
- setImmutable() - Method in class org.intermine.objectstore.query.Results
-
Tells this Results object that it is being put into a cache, so it needs to be made immutable
to prevent threads stomping on each other and changing settings.
- setImplementations(String) - Method in class org.intermine.xml.full.Item
-
Set the "implements" of this item.
- setIncludeHeaders(boolean) - Method in class org.intermine.web.struts.TableExportForm
-
Set the includeHeaders flag.
- setIndex(int) - Method in class org.intermine.api.results.Column
-
Sets the value of index
- setInputModelFile(File) - Method in class org.intermine.task.ModelMergerTask
-
Set the model to add additions to.
- setIntactOrganisms(String) - Method in class org.intermine.bio.dataconversion.PsiConverter
-
Sets the list of taxonIds that should be imported if using split input files.
- setIntegrationWriter(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
-
Set the IntegrationWriter.
- setIntegrationWriter(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
-
Set the IntegrationWriter.
- setIntegrationWriterAlias(String) - Method in class org.intermine.task.DirectDataLoaderTask
-
Set the IntegrationWriter.
- setInterMineAPI(ServletContext, InterMineAPI) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Sets the InterMineAPI in the servlet context.
- setIntroText(String) - Method in class org.intermine.web.logic.aspects.Aspect
-
Set the introduction text
- setInvite(String) - Method in class org.intermine.web.struts.InvitationForm
-
- setIsoform(boolean) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setItemRgb(int) - Method in class org.intermine.bio.io.bed.BEDRecord
-
- setItemRgb(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- setJavaClass(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Set the Java class name of the controller for this displayer.
- setJoinType(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
- setJSONContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets the content type to "application/json"
- setJSONFormat() - Method in class org.intermine.webservice.client.core.RequestImpl
-
Set the format as JSON-Object format.
- setJSONHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets the response header and content type for json output
- setJSONHeader(HttpServletResponse, String, boolean) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets the response header and content type for json output
- setJSONPContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets the content type to "text/javascript"
- setJSONPHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets the response header and content type for jsonp output
- setJSONRowsFormat() - Method in class org.intermine.webservice.client.core.RequestImpl
-
Set the format as JSON-Rows format.
- setJSONSchemaContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets the content type to "application/schema+json"
- setJSONSchemaHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Set the header for a JSON-schema response.
- setJspName(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Set the name of the JSP associated with this displayer.
- setKeggOrganisms(String) - Method in class org.intermine.bio.dataconversion.KeggPathwayConverter
-
Sets the list of taxonIds that should be imported
- setKeyFieldNames(List<String>) - Method in class org.intermine.api.profile.InterMineBag
-
Set the keyFieldNames
- setKeystoreFile(String) - Method in class org.intermine.web.task.KeyStoreTask
-
Bean-style setter for keystoreFile, as per ant spec.
- setKeyToRetreive(String) - Method in class org.intermine.task.RetrieveMetadataTask
-
Set a key to retrieve from database.
- setKeywords(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setLabel(String) - Method in class org.intermine.web.logic.config.FieldConfig
-
Set the label for this field-configuration.
- setLabel(String) - Method in class org.intermine.web.logic.config.Type
-
Set the label property.
- setLabel(String) - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Set the label of the constraint.
- setLabel(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- setLabel(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setLargeImage(String) - Method in class org.intermine.web.logic.aspects.Aspect
-
Set the webapp relative path to the large image.
- setLayout(String) - Method in class org.intermine.web.logic.template.TemplateResultInput
-
- setLayout(String) - Method in class org.intermine.webservice.server.query.result.QueryResultInput
-
- setLdr(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setLength(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setLimit(int) - Method in class org.intermine.objectstore.query.Query
-
Sets the LIMIT parameter for this query - note that this is only honoured in a subquery.
- setLimit(Integer) - Method in class org.intermine.webservice.server.WebServiceInput
-
Sets maximum of returned results.
- setLimitOffset(int, int) - Method in class org.intermine.sql.query.Query
-
Sets the LIMIT and OFFSET numbers for this query.
- setLineLength(Integer) - Method in class org.intermine.web.logic.config.InlineListConfig
-
Sets the amount of entries to show based on their total length
- setLink(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setLink(String) - Method in class org.intermine.web.struts.WidgetForm
-
- setLinkFile(File) - Method in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask
-
Set the linkFile attribute.
- setLinkRedirect(String) - Method in class org.intermine.api.results.ResultElement
-
- setListLeft(String) - Method in class org.intermine.web.struts.ModifyBagForm
-
- setListPath(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- setListRight(String) - Method in class org.intermine.web.struts.ModifyBagForm
-
- setListsButton(String) - Method in class org.intermine.web.struts.ModifyBagForm
-
- setListSize(Integer) - Method in class org.intermine.webservice.server.lists.ListUploadService
-
Sets the size of the list on the header attributes.
- setLoadfragments(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
-
Toggle whether or not to load fragments.
- setLoadFullRecord(String) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
-
Load summary version of Publication record by default.
- setLoadtrembl(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
-
Toggle whether or not to load trembl data for all given organisms
- setLocation(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Set the location item for this record.
- setLog(Writer) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Allows the log to be set in this objectstore.
- setLog(Writer) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Not implemented.
- setLogBeforeExecute(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Sets the logBeforeExecute configuration option.
- setLogBeforeExecute(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Sets the logBeforeExecute configuration option.
- setLogEverything(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Sets the logEverything configuration option.
- setLogEverything(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Sets the logEverything configuration option.
- setLogExplains(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Sets the logExplains configuration option.
- setLogExplains(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Sets the logExplains configuration option.
- setLogTableName(String) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Allows the log table name to be set in this objectstore.
- setLogTableName(String) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Not implemented.
- setLoopQueryOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Sets the value of loopQueryOp
- setLoopQueryValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Sets the value of loopQueryValue
- setMailinglist(boolean) - Method in class org.intermine.web.struts.CreateAccountForm
-
- setMainTitles(String) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
-
Set main title(s) path(s) for the object, e.g.: symbol, primaryIdentifier => eve FBgn0000606
- setMatchIDs(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm
-
Set the encoded match ids.
- setMatchOnFirst(boolean) - Method in class org.intermine.api.bag.BagQueryConfig
-
If flag is true, bagqueryrunner queries for identifier until match is found, returning
only that first matching record.
- setMaterialisedCollection(Collection<E>) - Method in class org.intermine.objectstore.proxy.ProxyCollection
-
Sets the collection with a new materialised collection.
- setMax(int) - Method in class org.intermine.objectstore.query.ResultsInfo
-
Sets the maximum possible number of rows in the results.
- setMax(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setMax(String) - Method in class org.intermine.web.struts.WidgetForm
-
- setMaxCount(int) - Method in class org.intermine.webservice.client.core.RequestImpl
-
Sets the maximum number of rows returned.
- setMaxP(double) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
-
- setMaxQueryParseTime(long) - Method in class org.intermine.sql.precompute.QueryOptimiserContext
-
Set the maximum time in milliseconds that the optimiser should spend parsing a query from
SQL string to an org.intermine.sql.Query object.
- setMessage(String) - Method in class org.intermine.web.struts.ContactForm
-
- setMethod(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
-
terms describe the method used int he experiment, eg two hybrid, etc
- setMethod(String) - Method in class org.intermine.task.StaticMethodTask
-
Name of method to call.
- setMin(int) - Method in class org.intermine.objectstore.query.ResultsInfo
-
Sets the minimum possible number of rows in the results.
- setMinBagTableSize(int) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Set the cutoff value used to decide if a bag should be put in a table.
- setMinBagTableSize(int) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Set the cutoff value used to decide if a bag should be put in a table.
- setMineId(Integer) - Method in class org.intermine.webservice.server.lists.ListsServiceInput
-
Sets Intermine unique object id
- setMinRows(int) - Method in class org.intermine.objectstore.intermine.ParallelPrecomputer
-
Set the minimum row count for precomputed queries.
- setMinRows(Integer) - Method in class org.intermine.task.PrecomputeTask
-
Set the minimum row count for precomputed queries.
- setMinRows(Integer) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
-
Set the minimum row count for precomputed queries.
- setMissingChromosomeLocations() - Method in class org.intermine.bio.postprocess.CalculateLocations
-
For each SequenceFeature, if it has a Location on a Chromosome, set the
SequenceFeature.chromosomeLocation reference *if* the reference is not already set.
- setMode(String) - Method in class org.intermine.sql.precompute.QueryOptimiserContext
-
Sets the optimiser mode of operation.
- setModel(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
-
Set the name of model to create data in
- setModel(Model) - Method in class org.intermine.pathquery.Node
-
Attach the model.
- setModel(String) - Method in class org.intermine.task.AnalyseDbTask
-
Set model name, must be set if class name specified
- setModel(String) - Method in class org.intermine.task.BuildDbTask
-
Sets the model
- setModel(String) - Method in class org.intermine.task.ModelOutputTask
-
Set the model to be used.
- setModel(Model) - Method in class org.intermine.web.logic.query.MetadataNode
-
- setModel(Model) - Method in class org.intermine.xml.full.Item
-
Set the Model to use when checking calls to the other set methods
- setModelName(String) - Method in class org.intermine.task.ConverterTask
-
Set the target model name
- setModelName(String) - Method in class org.intermine.task.StoreMetadataTask
-
Sets the model name
- setMolecularWeight(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setMonkey(String) - Method in class org.intermine.web.struts.ContactForm
-
- setMultiValueAttribute(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Sets the value of multiValueAttribute, a string representing the values selected
by the user separated by a comma.
- setMultiValueAttribute(Map<String, String>) - Method in class org.intermine.web.struts.TemplateForm
-
Set the multivalueattribute
- setMultiValueAttribute(String, String) - Method in class org.intermine.web.struts.TemplateForm
-
Set the multivalueattribute
- setMultivalues(List<String>) - Method in class org.intermine.web.logic.template.ConstraintInput
-
Set multivalues
- setMultiValues(Map<String, String[]>) - Method in class org.intermine.web.struts.TemplateForm
-
Set the multiValues
- setMultiValues(String, String[]) - Method in class org.intermine.web.struts.TemplateForm
-
Set a multiselect attribute value
- setName(String) - Method in class org.intermine.api.beans.ObjectDetails
-
- setName(String) - Method in class org.intermine.api.profile.InterMineBag
-
Set the value of name
- setName(String) - Method in class org.intermine.api.template.ApiTemplate
-
- setName(String) - Method in class org.intermine.bio.chado.ChadoCVTerm
-
Set the name of this term.
- setName(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setName(String) - Method in class org.intermine.bio.io.bed.BEDRecord
-
- setName(String) - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- setName(String) - Method in class org.intermine.bio.ontology.OboTypeDefinition
-
- setName(String) - Method in class org.intermine.template.TemplateQuery
-
Sets the query short name.
- setName(String) - Method in class org.intermine.web.logic.aspects.Aspect
-
Set the data set name.
- setName(String) - Method in class org.intermine.web.logic.aspects.AspectSource
-
Set the source name.
- setName(String) - Method in class org.intermine.web.logic.template.TemplateResultInput
-
Sets template name.
- setName(String) - Method in class org.intermine.web.struts.ContactForm
-
- setName(String) - Method in class org.intermine.web.struts.TemplateForm
-
Set the template name.
- setName(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
-
- setName(String) - Method in class org.intermine.webservice.client.services.TemplateService.TemplateRequest
-
Sets the name of the template to be used.
- setName(String) - Method in class org.intermine.xml.full.Attribute
-
Set the name of this field
- setName(String) - Method in class org.intermine.xml.full.Reference
-
Set the name of this field
- setName(String) - Method in class org.intermine.xml.full.ReferenceList
-
Set the name of this field.
- setNameSource(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
-
- setNamespace(String) - Method in class org.intermine.bio.ontology.OboTerm
-
Set the namespace attribute.
- setNameSpace(String) - Method in class org.intermine.webservice.server.WebService
-
Set the default name-space for configuration property look-ups.
- setNewBagName(String) - Method in class org.intermine.api.bag.operations.BagOperation
-
- setNewBagName(String) - Method in class org.intermine.web.struts.BagUploadConfirmForm
-
Set the bag name.
- setNewBagName(String) - Method in class org.intermine.web.struts.ModifyBagForm
-
Set the new bag name.
- setNewBagName(String) - Method in class org.intermine.web.struts.SaveBagForm
-
Sets the value of newBagName
- setNewBagType(String) - Method in class org.intermine.web.struts.TriageBagForm
-
Set the new bag name.
- setNewpassword(String) - Method in class org.intermine.web.struts.ChangePasswordForm
-
The new password
- setNewpassword(String) - Method in class org.intermine.web.struts.PasswordResetForm
-
Sets the value of newpassword.
- setNewpassword2(String) - Method in class org.intermine.web.struts.ChangePasswordForm
-
New password verification
- setNewpassword2(String) - Method in class org.intermine.web.struts.PasswordResetForm
-
Sets the value of newpassword2.
- setNextEnabled(boolean) - Method in class org.intermine.web.tags.table.NavigationBarTag
-
- setNoCache(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets that the result must not be cached.
- setNoCacheEnforced(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets enforced no-cache headers to completely disable cache for this response.
- setNoExplain() - Method in interface org.intermine.objectstore.proxy.LazyCollection
-
Sets this LazyCollection to bypass the explain check in ObjectStore.execute().
- setNoExplain() - Method in class org.intermine.objectstore.proxy.ProxyCollection
-
Sets this LazyCollection to bypass the explain check in ObjectStore.execute().
- setNoExplain() - Method in class org.intermine.objectstore.query.Results
-
Sets this Results object to bypass the explain check in ObjectStore.execute().
- setNoOptimise() - Method in interface org.intermine.objectstore.proxy.LazyCollection
-
Sets this LazyCollection to bypass the optimiser
- setNoOptimise() - Method in class org.intermine.objectstore.proxy.ProxyCollection
-
Sets this LazyCollection to bypass the optimiser
- setNoOptimise() - Method in class org.intermine.objectstore.query.Results
-
Sets this Results object to bypass the optimiser.
- setNoPrefetch() - Method in class org.intermine.objectstore.query.Results
-
Tells this Results object to never do any background prefetching.
- setNoResultsMessage(String) - Method in class org.intermine.web.tags.table.TableTag
-
- setNotAnalysed(int) - Method in class org.intermine.web.logic.widget.HTMLWidget
-
- setNotAnalysed(int) - Method in class org.intermine.web.logic.widget.Widget
-
- setNullConstraint(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Set the null/not null constraint.
- setNullConstraint(Map<String, Object>) - Method in class org.intermine.web.struts.TemplateForm
-
Set the nullConstraint
- setNullConstraint(String, String) - Method in class org.intermine.web.struts.TemplateForm
-
Set a nullConstraint
- setNumberOfMainTitlesToShow(Integer) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
-
How many main titles to show in the main title
- setNumberOpt(String) - Method in class org.intermine.web.struts.WidgetForm
-
- setOAuth2Providers(ServletContext, Set<String>) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Set the set of supported OAuth2 providers to use.
- setoBJECT(String, ObjectStore) - Method in interface org.intermine.model.InterMineObject
-
Sets the values of the fields to the values in the given NotXml.
- setoBJECT(String[], ObjectStore) - Method in interface org.intermine.model.InterMineObject
-
Sets the values of the fields to the values in the given split NotXml.
- setoBJECT(String, ObjectStore) - Method in class org.intermine.objectstore.proxy.ProxyReference
-
Sets the values of the fields to the values in the given NotXml.
- setoBJECT(String[], ObjectStore) - Method in class org.intermine.objectstore.proxy.ProxyReference
-
Sets the values of the fields to the values in the given split NotXml.
- setObjectId(Integer) - Method in class org.intermine.web.logic.results.InlineResultsTableRow
-
Set imObj ID for the object (taken from the first valid imObj id for this row)
- setObjects(Set<ObjectDetails>) - Method in class org.intermine.api.beans.PartnerLink
-
- setObjectStore(ObjectStore) - Method in class org.intermine.objectstore.translating.Translator
-
Set this Translator's ObjectStore.
- setObjectStore(ObjectStore) - Method in class org.intermine.task.CreateIndexesTask
-
Set the ObjectStore to use.
- setObjectStore(ObjectStore) - Method in class org.intermine.web.task.CreateSearchIndexTask
-
Set the object store.
- setObjectStoreAlias(String) - Method in class org.intermine.web.task.EvictOrphansTask
-
Bean-style setter so that any can do its stuff.
- setObjectStoreWriter(String) - Method in class org.intermine.bio.postprocess.FlyBaseUniProtRefsTask
-
Sets the value of objectStoreWriter
- setObjectStoreWriter(String) - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask
-
Sets the value of objectStoreWriter
- setOboRelations(List<OboRelation>) - Method in class org.intermine.bio.dataconversion.OboConverter
-
- setOboTerms(Collection<OboTerm>) - Method in class org.intermine.bio.dataconversion.OboConverter
-
- setObsolete(boolean) - Method in class org.intermine.bio.ontology.OboTerm
-
Set the obsolete flag for this OboTerm as read from an OBO file.
- setOldModelLocation(String) - Method in class org.intermine.web.task.ModelUpdateTask
-
Set the location of the previous model.
- setOldpassword(String) - Method in class org.intermine.web.struts.ChangePasswordForm
-
The old password
- setOnClick(String) - Method in class org.intermine.web.tags.disclosure.DisclosureTag
-
- setOntologyName(String) - Method in class org.intermine.bio.task.OboConverterTask
-
Set the name of the ontology
- setOntologyPrefix(String) - Method in class org.intermine.bio.dataconversion.OboConverter
-
The prefix of ontology terms to be processed.
- setOpenByDefault(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
-
Set whether this field should be uncollapsed if
sectionOnRight is true.
- setOpened(boolean) - Method in class org.intermine.web.tags.disclosure.DisclosureTag
-
Sets new state of disclosure.
- setOpenIdProviders(ServletContext, Set<String>) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Set the set of supported Open-ID providers to use.
- setOperation(String) - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask
-
Sets the value of operation
- setOperationButton(String) - Method in class org.intermine.web.struts.SaveBagForm
-
- setOperator(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Set the operator, "and" or "or"
- setOptions(String) - Method in class org.intermine.web.task.KeyStoreTask
-
Bean-style setter for optionsFile, as per ant spec.
- setOptionsTileName(String) - Method in class org.intermine.web.logic.config.TableExportConfig
-
Set the optionsTileName of this TableExportConfig
- setOrCheckClass(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
-
Set the class, or if one is already set on the map, check that this one is valid for it.
- setOrCheckClassAndId(ResultElement, Path, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
-
Sets the basic information (class and objectId) on the jsonMap provided.
- setOrCheckId(ResultElement, Map<String, Object>) - Method in class org.intermine.webservice.server.output.JSONResultsIterator
-
Set the id, or if one is already set, check that it matches the one on the map.
- setOrganism(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Set organism item, this is global across record handler and final
- setOrganisms(String) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
-
Set the taxon ids to use when creating the Organism Item for the new features.
- setOrganisms(String) - Method in class org.intermine.bio.dataconversion.UniprotFilterTask
-
A space separated list of NCBI taxon ids to include in the filter output.
- setOrganisms(String) - Method in class org.intermine.bio.postprocess.IntronUtil
-
Set a comma separated list of taxon ids to create introns for.
- setOrgTaxonId(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
-
Set the organism taxon id
- setOriginalConstraint(PathConstraint) - Method in class org.intermine.web.logic.query.DisplayConstraint
-
- setOsAlias(String) - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
-
Set the ObjectStore alias.
- setOsAlias(String) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
-
Set the ObjectStore alias.
- setOsAlias(String) - Method in class org.intermine.task.StaticMethodTask
-
Set the os alias.
- setOSAlias(String) - Method in class org.intermine.web.task.CreateSearchIndexTask
-
Set the alias of the main object store.
- setOSAlias(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
-
Set the alias of the main object store.
- setOSAlias(String) - Method in class org.intermine.web.task.LoadBagValuesTask
-
Set the alias of the main object store.
- setOSAlias(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
-
Set the alias of the main object store.
- setOSAlias(String) - Method in class org.intermine.web.task.ModelUpdateTask
-
Set the alias of the main object store.
- setOSAlias(String) - Method in class org.intermine.web.task.ProfileReadTask
-
Set the alias of the main object store.
- setOSAlias(String) - Method in class org.intermine.web.task.ProfileWriteTask
-
Set the alias of the main object store.
- setOSAlias(String) - Method in class org.intermine.web.task.UpdateListTablesTask
-
Set the alias of the main object store.
- setOsb(ObjectStoreBag) - Method in class org.intermine.api.profile.InterMineBag
-
Sets the ObjectStoreBag.
- setOsName(String) - Method in class org.intermine.bio.task.OboConverterTask
-
Set the objectstore name
- setOsName(String) - Method in class org.intermine.objectstore.intermine.TorqueModelOutputTask
-
Set the ObjectStore for which to generate the data.
- setOsName(String) - Method in class org.intermine.task.AnalyseDbTask
-
Set the database alias
- setOsName(String) - Method in class org.intermine.task.BuildDbTask
-
Sets the objectstore
- setOsName(String) - Method in class org.intermine.task.ConverterTask
-
Set the objectstore name
- setOsName(String) - Method in class org.intermine.task.PostProcessorTask
-
Set the ObjectStore alias.
- setOsName(String) - Method in class org.intermine.task.RetrieveMetadataTask
-
Sets the os alias
- setOsName(String) - Method in class org.intermine.task.StoreMetadataTask
-
Sets the database alias
- setOut(OutputStream) - Method in class org.intermine.web.task.KeyStoreTask
-
Set the output handler.
- setOuterInSummary(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
-
- setOuterJoin(boolean) - Method in class org.intermine.pathquery.Node
-
Sets whether this should be an outer join.
- setOuterJoins(PathQuery, String) - Method in class org.intermine.pathquery.PathQueryHandler
-
Given a path that may contain ':' characters to represent outer joins,
find each : separated segment and set the status for that join to OUTER.
- setOuterJoinStatus(String, OuterJoinStatus) - Method in class org.intermine.pathquery.PathQuery
-
Sets the outer join status of the last part of a given path in this query.
- setOutputFile(String) - Method in class org.intermine.bio.dataconversion.EntrezOrganismRetriever
-
Set the output file name
- setOutputFile(String) - Method in class org.intermine.bio.dataconversion.EntrezPublicationsRetriever
-
Set the output file name
- setOutputFile(File) - Method in class org.intermine.bio.postprocess.PostProcessOperationsTask
-
Sets the value of outputFile
- setOutputFile(File) - Method in class org.intermine.bio.task.SOClassNameMapMakerTask
-
Sets the value of outputFile.
- setOutputFile(File) - Method in class org.intermine.bio.task.SOToModelTask
-
Set the output file to write generated additions XML to.
- setOutputFile(File) - Method in class org.intermine.task.AcceptanceTestTask
-
Set the File to write output to
- setOutputFile(File) - Method in class org.intermine.task.ModelMergerTask
-
Path of file to write resulting model to.
- setOutputFile(File) - Method in class org.intermine.task.SummariseObjectStoreTask
-
Set the name of the file to write the summary into
- setOverwriting(boolean) - Method in class org.intermine.web.struts.ImportTagsForm
-
Set the overwriting flag.
- setOverwriting(boolean) - Method in class org.intermine.web.struts.TemplatesImportForm
-
Set the overwriting flag.
- setPackageName(String) - Method in class org.intermine.objectstore.query.iql.IqlQuery
-
Set the package name
NOTE: this method is merely here to make this a Bean.
- setPage(Page) - Method in interface org.intermine.webservice.client.core.Request
-
Set the page for this request.
- setPage(Page) - Method in class org.intermine.webservice.client.core.RequestImpl
-
Specify what section of the result set you wish to retrieve.
- setPageAndPageSize(int, int) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Set the page size and page together.
- setPageName(String) - Method in class org.intermine.web.struts.ModifyBagForm
-
- setPageName(String) - Method in class org.intermine.web.struts.ModifyTemplateForm
-
- setPageSize(int) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Set the page size of the table
- setPageSize(String) - Method in class org.intermine.web.struts.ChangeTableSizeForm
-
Set the page size
- setPageSize(Integer) - Method in class org.intermine.web.tags.table.NavigationBarTag
-
- setParameter(String, String) - Method in interface org.intermine.webservice.client.core.Request
-
Sets parameter
- setParameter(String, String) - Method in class org.intermine.webservice.client.core.RequestImpl
-
Sets parameter
- setParameterName(String) - Method in class org.intermine.web.logic.template.ConstraintInput
-
- setParameters(List<?>) - Method in class org.intermine.objectstore.query.iql.IqlQuery
-
Set the parameters
- setParameters(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
A JSON string representing custom parameters for this displayer.
- setParentTermId(String) - Method in class org.intermine.bio.ontology.OboRelation
-
- setPassword(String, String) - Method in class org.intermine.api.profile.ProfileManager
-
Change a user's password
A check should be made prior to this call to ensure a Profile exists
- setPassword(String) - Method in class org.intermine.web.struts.CreateAccountForm
-
- setPassword(String) - Method in class org.intermine.web.struts.LoginForm
-
Sets the value of password
- setPassword(String) - Method in class org.intermine.webservice.server.WebServiceInput
-
- setPassword2(String) - Method in class org.intermine.web.struts.CreateAccountForm
-
- setPath(String) - Method in class org.intermine.web.logic.config.InlineListConfig
-
Path set from WebConfig, ie "probeSets.primaryIdentifier"
- setPath(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Sets the value of path
- setPathConstraints(String, List<? super PathConstraint>) - Static method in class org.intermine.web.logic.widget.config.WidgetConfig
-
Turn a string representing a set of constraints into a list of constraints.
- setPathId(String) - Method in class org.intermine.web.logic.template.ConstraintInput
-
- setPathQuery(PathQuery) - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
-
- setPathsString(String) - Method in class org.intermine.web.struts.TableExportForm
-
Set the paths string
- setPathStrings(String) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
- setPdbOrganisms(String) - Method in class org.intermine.bio.dataconversion.PdbConverter
-
Sets the list of taxonIds that should be imported if using split input files.
- setPerm(String) - Method in class org.intermine.task.GrantTask
-
The permission to grant: SELECT, INSERT, UPDATE, DELETE, RULE,
REFERENCES, TRIGGER, ALL
- setPlacement(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Set the data category name under which this displayer should appear.
- setPlainTextContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets plain text content type.
- setPlainTextHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets response header and content type for plain text output.
- setPopulationBagName(String) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
-
Set the bag's name for reference population
- setPreference(Profile, String, String) - Method in class org.intermine.api.profile.PreferencesManager
-
- SetPreferencesService - Class in org.intermine.webservice.server.user
-
A service to set one or more preferences for a user.
- SetPreferencesService(InterMineAPI) - Constructor for class org.intermine.webservice.server.user.SetPreferencesService
-
- setPrefix(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
-
Only used for MGI for now
- setPrimaryIdentifier(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setProcessors(String) - Method in class org.intermine.bio.dataconversion.ChadoDBConverter
-
Set the class names of the ChadoProcessors to run.
- setProfile(HttpSession, Profile) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Sets the user profile in the session.
- setProfileId(Integer) - Method in class org.intermine.api.profile.InterMineBag
-
Sets the profileId - moves this bag from one profile to another.
- setPropertiesOrigins(ServletContext, Map<String, List<String>>) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Sets the origins of the web properties on the servlet context.
- setPropertyName(String) - Method in class org.intermine.web.struts.EditPropertiesForm
-
Set the property name.
- setPropertyValue(String) - Method in class org.intermine.web.struts.EditPropertiesForm
-
Set the value of the property
- setProteinNames(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setPublication(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
-
- setPublicId(String) - Method in class org.intermine.webservice.server.lists.ListsServiceInput
-
Sets id of object.
- setPubmedOrganisms(String) - Method in class org.intermine.bio.dataconversion.PubMedGeneConverter
-
Sets the list of taxonIds that should be imported
- setPubs(List<String>) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setPValue(String) - Method in class org.intermine.web.struts.WidgetForm
-
- setQuery(String) - Method in class org.intermine.task.RunIqlQueryTask
-
An query string to execute, may be IQL or SQL by format parameter must be set correctly,
richard
- setQuery(HttpSession, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Set the current query on the session.
- setQuery(String) - Method in class org.intermine.web.struts.QueryForm
-
- setQueryBuilder(String) - Method in class org.intermine.web.struts.ImportQueriesForm
-
Set the queryBuilder field.
- setQueryClass(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
-
If the name of a class is set will only load objects of that type.
- setQueryInfo(PathQuery, ResultsInfo) - Method in class org.intermine.api.query.WebResultsExecutor
-
Sets a ResultsInfo entry in the infoCache for a given PathQuery.
- setQueryName(String) - Method in class org.intermine.web.struts.SaveQueryForm
-
Set the query name
- setQueryString(String) - Method in class org.intermine.objectstore.query.iql.IqlQuery
-
Set the query String
NOTE: this method is merely here to make this a Bean.
- setQueryXml(String) - Method in class org.intermine.webservice.client.services.QueryService.QueryRequest
-
Adds the query to be run.
- setRangeConstraint(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Set the range constraint value.
- setRangeLabel(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
Set the value of rangeLabel
- setRangeOp(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
- setRedundant(boolean) - Method in class org.intermine.bio.ontology.OboRelation
-
- setReference(String, String) - Method in class org.intermine.xml.full.Item
-
Add a reference to this item.
- setReference(String, Item) - Method in class org.intermine.xml.full.Item
-
Add a reference that points to a particular item.
- setRefId(String) - Method in class org.intermine.xml.full.Reference
-
Set the refId of this field
- setRefIds(List<String>) - Method in class org.intermine.xml.full.ReferenceList
-
Set the references in this collection
- setRelationship(OboTypeDefinition) - Method in class org.intermine.bio.ontology.OboRelation
-
- setReplacesFields(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Set the comma separated list of field names that should not be displayed on the report page
when this displayer is used.
- setResponseHeader(HttpServletResponse, boolean) - Method in class org.intermine.web.logic.export.http.CSVHttpExporter
-
Sets header and content type of result in response.
- setResponseHeader(HttpServletResponse, boolean) - Method in class org.intermine.web.logic.export.http.StandardHttpExporter
-
Sets header and content type of result in response.
- setResponseHeader(HttpServletResponse, boolean) - Method in class org.intermine.web.logic.export.http.TabHttpExporter
-
Sets header and content type of result in response.
- setResultsTable(HttpSession, String, PagedTable) - Static method in class org.intermine.web.logic.session.SessionMethods
-
- setRetryCount(int) - Method in class org.intermine.webservice.client.util.HttpConnection
-
Sets retry count.
- setReturnToString(String) - Method in class org.intermine.web.struts.LoginForm
-
Sets the URL to return to if the login is successful.
- setRowFormatter(RowFormatter) - Method in class org.intermine.webservice.server.output.FlatFileFormatter
-
Set the row formatter
- setRows(int) - Method in class org.intermine.objectstore.query.ResultsInfo
-
Sets the estimated number of rows in the results.
- setRows(List<List<String>>) - Method in class org.intermine.web.tags.table.TableTag
-
Set table rows.
- setRowSpan(Integer) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
-
Set how many rows this identifier spans
- setSavedTemplateQuery(SavedTemplateQuery) - Method in class org.intermine.api.template.ApiTemplate
-
Sets the saved template query object.
- setSavePopulation(boolean) - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput.Builder
-
- setSchemafile(String) - Method in class org.intermine.task.BuildDbTask
-
Adds the schemafile to be processed.
- setScope(String) - Method in class org.intermine.web.struts.TemplateForm
-
Set the template scope.
- setScore(int) - Method in class org.intermine.bio.io.bed.BEDRecord
-
- setScore(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- setSectionOnRight(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
-
Set whether this field should be rendered in its own section on
the right side of the page.
- setSectionTitle(String) - Method in class org.intermine.web.logic.config.FieldConfig
-
Set the section title (if sectionOnRight == true).
- setSelectable(boolean) - Method in class org.intermine.api.results.Column
-
Sets the value of selectable
- setSelected(boolean) - Method in class org.intermine.web.logic.query.MetadataNode
-
Sets the value of selected
- setSelected(String[]) - Method in class org.intermine.web.struts.ModifyTemplateForm
-
Sets the selected templates
- setSelected(String[]) - Method in class org.intermine.web.struts.WidgetForm
-
- setSelectedBagOp(ConstraintOp) - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Set the seletedBagOp
- setSelectedBags(String[]) - Method in class org.intermine.web.struts.ModifyBagForm
-
Sets the selected bags
- setSelectedBagValue(String) - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Set the seletedBagValue returned bye the getSelectedValue if the bag is selected
- setSelectedClass(String) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
- setSelectedColumn(int) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
- setSelectedElements(String[]) - Method in class org.intermine.web.struts.ModifyBagDetailsForm
-
Set the list of selectedElements
- setSelectedExtraAttribute(String) - Method in class org.intermine.web.struts.WidgetForm
-
- setSelectedObjects(String[]) - Method in class org.intermine.web.struts.BagUploadConfirmForm
-
Sets the ids of the selected objects - ie. those that should be included in the new bag
- setSelectedObjects(String[]) - Method in class org.intermine.web.struts.SaveBagForm
-
Sets the selected objects
- setSelectedQueries(String[]) - Method in class org.intermine.web.struts.ModifyQueryForm
-
Sets the selected queries
- setSelectionIds(Map<Integer, String>) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
- setSeqClsName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
-
Set the sequenceClassName
- setSeqDataSourceName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
-
Set the seqDataSourceName
- setSeqHandlerClassName(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
-
Set the name of GFF3SeqHandler to use when processing.
- setSequence(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Set sequence item created for this record, should not be edited in handler.
- setSequence(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setSequenceType(String) - Method in class org.intermine.bio.dataconversion.FastaLoaderTask
-
Set the sequence type to be passed to the FASTA parser.
- setSeriesLabels(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- setSeriesPath(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- setSeriesValues(String) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- setServiceUrl(String) - Method in interface org.intermine.webservice.client.core.Request
-
Sets service URL.
- setServiceUrl(String) - Method in class org.intermine.webservice.client.core.RequestImpl
-
Sets service URL.
- setSession(HttpSession) - Method in class org.intermine.web.logic.widget.config.GraphWidgetConfig
-
- setShowExtraConstraint(boolean) - Method in class org.intermine.web.logic.query.DisplayConstraint
-
- setShowIdentifier(Boolean) - Method in class org.intermine.web.logic.results.BagUploadConfirmInlineResultsTableRow
-
Set to show the identifier in this row
- setShowImmediately(Boolean) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Set if we should display the displayer immediately
- setShowInHeader(Boolean) - Method in class org.intermine.web.logic.config.InlineListConfig
-
Show this list in the header?
- setShowInInlineCollection(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
-
Set the showInInlineCollection flag.
- setShowInListAnalysisPreviewTable(Boolean) - Method in class org.intermine.web.logic.config.FieldConfig
-
Specify if we want to show this field for an object in list analysis page table preview
- setShowInQB(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
-
Shall we show this field in a QueryBuilder?
- setShowInResults(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
-
Set the showInResults flag.
- setShowInSummary(boolean) - Method in class org.intermine.web.logic.config.FieldConfig
-
Set the showInSummary flag.
- setShowLinksToObjects(Boolean) - Method in class org.intermine.web.logic.config.InlineListConfig
-
Shall we show links to the objects's report pages?
- setShowOnLeft(String) - Method in class org.intermine.web.logic.config.Displayer
-
- setSingleton(boolean) - Method in class org.intermine.objectstore.query.QueryCollectionPathExpression
-
Sets whether the collection should be a singleton collection, or whether it should be a
collection of ResultRows.
- setSize(int) - Method in class org.intermine.webservice.server.lists.FlatListFormatter
-
- setSize(int) - Method in class org.intermine.webservice.server.lists.HtmlListFormatter
-
- setSize(int) - Method in class org.intermine.webservice.server.lists.JSONListFormatter
-
- setSize(int) - Method in interface org.intermine.webservice.server.lists.ListFormatter
-
set the size of the list.
- setSoFile(File) - Method in class org.intermine.bio.task.SOClassNameMapMakerTask
-
Sets the File containing the SO OBO data.
- setSoFile(File) - Method in class org.intermine.bio.task.SOToModelTask
-
Sets the File containing the SO OBO data.
- setSOTerm(DataConverter, Item, String, String) - Static method in class org.intermine.bio.dataconversion.BioStoreHook
-
For an item, set the SO term reference if one is not already set.
- setSoTermListFile(File) - Method in class org.intermine.bio.task.SOToModelTask
-
Set the file containing a list of SO terms to be added to the data model.
- setSource(Integer, String, Source) - Method in class org.intermine.dataloader.DataTracker
-
Set the Source for a field of an object in the database
- setSource(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
-
Set the ObjectStore that is the data source.
- setSource(Source) - Method in class org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl
-
Sets the source of the data, so we know what the primary keys are, and can fetch that extra
data.
- setSourceName(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
-
Set the source name, as used by primary key priority config.
- setSourceName(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
-
Set the source name, as used by primary key priority config.
- setSourceName(String) - Method in class org.intermine.task.DirectDataLoaderTask
-
Set the source name, as used by primary key priority config.
- setSourceName(String) - Method in class org.intermine.task.FullXmlConverterTask
-
Set the source name, as used by primary key priority config.
- setSourceType(String) - Method in class org.intermine.dataloader.ObjectStoreDataLoaderTask
-
Set the source type, as used by primary key priority config.
- setSourceType(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
-
Set the source type, as used by primary key priority config.
- setSourceType(String) - Method in class org.intermine.task.DirectDataLoaderTask
-
Set the source type, as used by primary key priority config.
- setSrc(String) - Method in class org.intermine.web.logic.config.Displayer
-
Set the source of this displayer
- setStart(int) - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
-
Set start value
- setStart(long) - Method in class org.intermine.objectstore.query.ResultsInfo
-
Sets the estimated amount of time taken to produce the first row of the results.
- setStart(int) - Method in class org.intermine.webservice.client.core.RequestImpl
-
Set the start parameter.
- setStart(Integer) - Method in class org.intermine.webservice.server.WebServiceInput
-
Sets from which index should be results returned 1-based.
- setStartClass(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- setStartClassDisplay(String) - Method in class org.intermine.web.logic.widget.config.EnrichmentWidgetConfig
-
- setStartingPoints(String) - Method in class org.intermine.web.logic.aspects.Aspect
-
Set the starting point class names as a space seperated list.
- setState(BagState) - Method in class org.intermine.api.profile.InterMineBag
-
Set bag state
- setState(String, String) - Static method in class org.intermine.dwr.AjaxServices
-
Set state that should be saved during the session.
- setState(String, Object) - Method in class org.intermine.web.logic.results.WebState
-
Set attribute.
- setStoreHook(DataConverterStoreHook) - Method in class org.intermine.dataconversion.DataConverter
-
Set a hook for this converter that will be called just before each Item is stored.
- setStrain(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
-
- setStrand(String) - Method in class org.intermine.bio.io.bed.BEDRecord
-
- setStrand(String) - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- setStrand(String) - Method in class org.intermine.bio.postprocess.CalculateLocations.SimpleLoc
-
Set strand value
- setStyle(String) - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
-
Sets element style.
- setStyleClass(String) - Method in class org.intermine.web.tags.disclosure.BaseDisclosureTag
-
Sets css style class of element.
- setSubclass(String) - Method in class org.intermine.web.logic.querybuilder.SummaryPath
-
Sets the subclass on this path.
- setSubclassValue(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Sets the value of subclassValue
- setSubject(String) - Method in class org.intermine.web.struts.ContactForm
-
- setSubject(String) - Method in class org.intermine.web.task.IssueTokenTask
-
Bean-style setter, as per the ant spec.
- setSubTitle(String) - Method in class org.intermine.web.logic.aspects.Aspect
-
Set the subtitle.
- setSubTitles(String) - Method in class org.intermine.web.logic.config.HeaderConfigTitle
-
Set subtitle(s) path(s) for the object, e.g.: organism.shortName => D. melanogaster
- setSubType(String) - Method in class org.intermine.webservice.client.core.ContentType
-
- setSummarise(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
-
Set the summarise flag.
- setSuperuser(boolean) - Method in class org.intermine.api.profile.Profile
-
Set the superuser flag and store it in userprofile database
- setSuperuserPassword(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
-
Set the superuser's initial password.
- setSuperUsers(String[]) - Method in class org.intermine.web.struts.ModifySuperUserForm
-
Sets the super users
- setSwitchable(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
- setSwitchOff(String, String) - Method in class org.intermine.web.struts.TemplateForm
-
Set the SwitchOff ability.
- setSwitchOffAbility(PathConstraint, SwitchOffAbility) - Method in class org.intermine.template.TemplateQuery
-
Sets the sbitch-off-ability of a constraint.
- setSwitchOffAbility(SwitchOffAbility) - Method in class org.intermine.web.logic.query.DisplayConstraint
-
Set the switchOffAbility
- setTabContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets tab separated values content type.
- setTabHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets response header and content type for tab separated
values output.
- setTable(String) - Method in class org.intermine.web.struts.TableExportForm
-
Set the table identifier to look up in the servlet context
- setTableDisplayer(Displayer) - Method in class org.intermine.web.logic.config.Type
-
Set the table displayer for this Type
- setTableid(String) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
- setTagValues(Map<?, ?>) - Method in class org.intermine.bio.ontology.OboTerm
-
Sets the variable holding the raw tagValues that created this Term.
- setTarget(String) - Method in class org.intermine.bio.task.GFF3ConverterTask
-
Set the target ObjectStore alias
- setTaxonId(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
-
- setTaxonId(String) - Method in class org.intermine.bio.dataconversion.UniprotEntry
-
- setTempdir(File) - Method in class org.intermine.task.BuildDbTask
-
Sets the directory for temporary files including sql output
- setTemplateButton(String) - Method in class org.intermine.web.struts.ModifyTemplateForm
-
- setTemplateLabel(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
Set the template label.
- setTemplateParameters(List<TemplateParameter>) - Method in class org.intermine.webservice.client.services.TemplateService.TemplateRequest
-
Set some template parameters.
- setTemplatesummary(List<Object>) - Method in class org.intermine.web.logic.query.DisplayConstraint
-
- setTemplatesXml(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
-
Set the templates xml file.
- setTermClass(String) - Method in class org.intermine.bio.task.OboConverterTask
-
Set the term class name
- setText(String) - Method in class org.intermine.web.logic.config.HeaderConfigLink
-
Set
- setText(String) - Method in class org.intermine.web.struts.BuildBagForm
-
Set the query string
- setTextToFind(String) - Method in class org.intermine.web.struts.FindInListForm
-
- setTgtDir(File) - Method in class org.intermine.bio.dataconversion.UniprotFilterTask
-
Set the target directory
- setTgtLocation(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Set the tgtLocation item for this record.
- setTgtOrganism(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Get the tgtOrganism item to use in this handler
- setTgtSequence(Item) - Method in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
Set tgtSequence item created for this record, should not be edited in handler.
- setThickEnd(int) - Method in class org.intermine.bio.io.bed.BEDRecord
-
- setThickEnd(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- setThickStart(int) - Method in class org.intermine.bio.io.bed.BEDRecord
-
- setThickStart(int) - Method in class org.intermine.bio.io.gaf.GAFRecord
-
- setThreshold(int) - Method in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
-
This sets the threshold above which a temp table will be used for deletes.
- setTileName(String) - Method in class org.intermine.web.logic.aspects.Aspect
-
Set the name of the tile/page to embed in the centre of the data set homepage.
- setTimeLimit(long) - Method in class org.intermine.sql.precompute.QueryOptimiserContext
-
Sets the optimiser's maximum effort time, in milliseconds.
- setTimeout(int) - Method in class org.intermine.webservice.client.util.HttpConnection
-
Sets timeout.
- settings - Variable in class org.intermine.sql.Database
-
- setTitle(String) - Method in class org.intermine.api.template.ApiTemplate
-
- setTitle(String) - Method in class org.intermine.pathquery.PathQuery
-
Sets the name of the query.
- setTitle(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- setTitle(String) - Method in class org.intermine.web.struts.EnrichmentWidgetForm
-
- setTitle(String) - Method in class org.intermine.web.struts.TemplateSettingsForm
-
Set the title
- setToggledElements(Map<String, Boolean>) - Method in class org.intermine.web.logic.results.WebState
-
Sets map of ids and its state.
- setToken(String) - Method in class org.intermine.web.struts.PasswordResetForm
-
Sets the value of token.
- setToken(String) - Method in class org.intermine.web.task.VerifyTokenTask
-
Bean-style setter for token, as per ant spec.
- setTrackQueue(Queue<Track>) - Method in class org.intermine.api.tracker.AbstractTracker
-
Set the queue of tracks
- setTransitive(boolean) - Method in class org.intermine.bio.ontology.OboTypeDefinition
-
- setTransitiveOver(List<String>) - Method in class org.intermine.bio.ontology.OboTypeDefinition
-
- setTreatColNames(boolean) - Method in class org.intermine.web.tags.table.TableTag
-
- setType(String) - Method in class org.intermine.api.beans.ObjectDetails
-
- setType(String) - Method in class org.intermine.api.profile.InterMineBag
-
- setType(String) - Method in class org.intermine.bio.io.gff3.GFF3Record
-
Set the type of this record.
- setType(String) - Method in class org.intermine.pathquery.Node
-
Set the value of type
- setType(String) - Method in class org.intermine.task.ModelOutputTask
-
Set the type of model output required.
- setType(String) - Method in class org.intermine.web.logic.query.MetadataNode
-
Set the value of type
- setType(String) - Method in class org.intermine.web.struts.BuildBagForm
-
Set the bag type
- setType(String) - Method in class org.intermine.web.struts.TableExportForm
-
Set the type
- setType(String) - Method in class org.intermine.web.tags.disclosure.DisclosureTag
-
Sets type of tag.
- setType(String) - Method in class org.intermine.webservice.client.core.ContentType
-
Sets main content type.
- setType(Request.RequestType) - Method in interface org.intermine.webservice.client.core.Request
-
- setType(Request.RequestType) - Method in class org.intermine.webservice.client.core.RequestImpl
- setType(String) - Method in class org.intermine.webservice.server.lists.ListsServiceInput
-
Sets object type.
- setTypeClass(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- setTypes(String) - Method in class org.intermine.web.logic.config.ReportDisplayerConfig
-
Set the types this displayer should be used for as a comma separated list of unqualified
class names.
- setUniprot(String) - Method in class org.intermine.bio.util.OrganismData
-
- setUniprotOrganisms(String) - Method in class org.intermine.bio.dataconversion.UniprotConverter
-
Sets the list of taxonIds that should be imported if using split input files.
- setUniqueIdentifier(String) - Method in class org.intermine.bio.dataconversion.UniprotConfig.ConfigEntry
-
- setUp() - Method in class org.intermine.task.CreateIndexesTask
-
Sets up the instance variables
- setupDatabase(Connection) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
-
Sets up the database for storing precomputed tables
- setupFieldValues() - Method in class org.intermine.web.logic.results.ReportObject
-
Setup fieldValues HashMap
- setUpPermission(InterMineAPI, ProfileManager.ApiPermission) - Static method in class org.intermine.web.logic.profile.LoginHandler
-
Does whatever needs to be done to a permissions object to get it ready
for a life cyle in a web service request.
- setUpProfile(HttpSession, String, String) - Static method in class org.intermine.web.logic.profile.LoginHandler
-
Initialises a profile for the current user based on their user name and password.
- setUpProfile(HttpSession, Profile) - Static method in class org.intermine.web.logic.profile.LoginHandler
-
Sets up a profile ready for a session in InterMine.
- setUrl(String) - Method in class org.intermine.bio.task.OboConverterTask
-
Set the url for the source of the ontology
- setUrl(String) - Method in class org.intermine.web.logic.aspects.AspectSource
-
Set the URL to source website.
- setUrl(String) - Method in class org.intermine.web.logic.config.HeaderConfigLink
-
Set
- setUrl(String) - Method in interface org.intermine.webservice.client.core.Request
-
Sets whole request URL.
- setUrl(String) - Method in class org.intermine.webservice.client.core.RequestImpl
-
Sets whole request URL.
- setUseBagConstraint(String, boolean) - Method in class org.intermine.web.struts.TemplateForm
-
Set value of useBagConstraint for given constraint key.
- setUseJoin(String) - Method in class org.intermine.web.struts.QueryBuilderConstraintForm
-
- setUser(String) - Method in class org.intermine.task.GrantTask
-
Set user to grant permissions to
- setUserId(Integer) - Method in class org.intermine.api.profile.Profile
-
Set the userId
- setUsername(String) - Method in class org.intermine.web.struts.CreateAccountForm
-
- setUsername(String) - Method in class org.intermine.web.struts.LoginForm
-
Sets the value of username
- setUsername(String) - Method in class org.intermine.web.struts.RequestPasswordForm
-
Sets the value of username
- setUsername(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
-
Set the account name to laod template to.
- setUsername(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
-
Set the account name to load template to.
- setUsername(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
-
Set the account name to laod template to.
- setUserName(String) - Method in class org.intermine.webservice.server.WebServiceInput
-
- setUserProfileAlias(String) - Method in class org.intermine.web.task.DumpDefaultTemplatesTask
-
Set the alias of the userprofile object store.
- setUserProfileAlias(String) - Method in class org.intermine.web.task.LoadBagValuesTask
-
Set the alias of the userprofile object store.
- setUserProfileAlias(String) - Method in class org.intermine.web.task.LoadDefaultTemplatesTask
-
Set the alias of the userprofile object store.
- setUserProfileAlias(String) - Method in class org.intermine.web.task.ModelUpdateTask
-
Set the alias of the userprofile object store.
- setUserProfileAlias(String) - Method in class org.intermine.web.task.PrecomputeTemplatesTask
-
Set the alias of the userprofile object store.
- setUserProfileAlias(String) - Method in class org.intermine.web.task.ProfileReadTask
-
Set the alias of the userprofile object store.
- setUserProfileAlias(String) - Method in class org.intermine.web.task.ProfileWriteTask
-
Set the alias of the userprofile object store.
- setUserProfileAlias(String) - Method in class org.intermine.web.task.TemplateTrackReadTask
-
Set the alias of the userprofile object store.
- setUserProfileAlias(String) - Method in class org.intermine.web.task.TemplateTrackWriteTask
-
Set the alias of the userprofile database.
- setUserProfileAlias(String) - Method in class org.intermine.web.task.UpdateListTablesTask
-
Set the alias of the userprofile object store.
- setUserProfileAlias(String) - Method in class org.intermine.web.task.UpdateTrackTableTask
-
Set the alias of the userprofile object store.
- setValue(String) - Method in class org.intermine.web.logic.template.ConstraintInput
-
Sets constraint value.
- setValue(B) - Method in class org.intermine.webservice.server.core.Pair
-
- setValue(String) - Method in class org.intermine.xml.full.Attribute
-
Set the value of this field
- setVerboseQueryLog(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Sets the verboseQueryLog configuration option.
- setVerboseQueryLog(boolean) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Sets the verboseQueryLog configuration option.
- setView(String) - Method in class org.intermine.web.struts.TemplateForm
-
Set the selected alternative view name.
- setViews(String) - Method in class org.intermine.web.logic.widget.config.WidgetConfig
-
- setVisible(boolean) - Method in class org.intermine.api.results.Column
-
Sets the value of visible
- setWebConfig(ServletContext, WebConfig) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Sets the WebConfig into the ServletContext.
- setWebConfig(WebConfig) - Method in class org.intermine.web.logic.widget.config.TableWidgetConfig
-
- setWebProperties(ServletContext, Properties) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Sets the web properties in the session.
- setWhichInput(String) - Method in class org.intermine.web.struts.BuildBagForm
-
Set the method the user used to upload her bag.
- setWidgetid(String) - Method in class org.intermine.web.struts.WidgetForm
-
- setWidgets(LinkedList) - Method in class org.intermine.web.logic.config.Type
-
- setWidgetTitle(String) - Method in class org.intermine.web.struts.WidgetForm
-
used on results page for description: "results for widget XYZ"
- setWriter(PrintWriter) - Method in class org.intermine.webservice.server.output.StreamedOutput
-
Sets associated writer
- setXml(String) - Method in class org.intermine.web.struts.ImportTagsForm
-
Set the xml.
- setXml(String) - Method in class org.intermine.web.struts.ImportXMLForm
-
Set the xml.
- setXml(String) - Method in class org.intermine.webservice.server.query.result.QueryResultInput
-
Sets xml query string.
- setXMLContentType(HttpServletResponse) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets XML content type.
- setXMLFormat() - Method in class org.intermine.webservice.client.core.RequestImpl
-
Set the format as XML format.
- setXMLHeader(HttpServletResponse, String) - Static method in class org.intermine.web.logic.export.ResponseUtil
-
Sets response header and content type for XML output.
- setXmlResource(String) - Method in class org.intermine.dataloader.XmlDataLoaderTask
-
Set XML resource name (to load data from classloader).
- setXmlResource(String) - Method in class org.intermine.task.FullXmlConverterTask
-
Set XML resource name (to load data from classloader).
- setXref(String) - Method in class org.intermine.bio.dataconversion.BioGridConverter.Config
-
- shareBagWithUser(String, String, String) - Method in class org.intermine.api.bag.BagManager
-
Share the bag given in input with the user which userName input
- shareBagWithUser(InterMineBag, Profile) - Method in class org.intermine.api.bag.BagManager
-
Let the recipient gain access to this bag in future uses of the application.
- shareBagWithUser(InterMineBag, String) - Method in class org.intermine.api.bag.SharedBagManager
-
Share the bag given in input with user which userName is given in input
- shareBagWithUser(String, String, String) - Method in class org.intermine.api.bag.SharedBagManager
-
Share the bag given in input with user which userName is given in input
To be used ONLY when deserialising the user-profile from XML.
- SHARED_BAGS - Static variable in class org.intermine.api.bag.SharedBagManager
-
the table name
- SharedBagBinding - Class in org.intermine.api.xml
-
Parse the shared bags in XML format
- SharedBagBinding() - Constructor for class org.intermine.api.xml.SharedBagBinding
-
- SharedBagHandler - Class in org.intermine.api.xml
-
Handle parsing of shared bags
- SharedBagHandler(List<Map<String, String>>) - Constructor for class org.intermine.api.xml.SharedBagHandler
-
Constructor
- SharedBagManager - Class in org.intermine.api.bag
-
Singleton manager class for shared bags.
- SharingBagUsersController - Class in org.intermine.web.struts
-
Controller for the inline tag editing tile
- SharingBagUsersController() - Constructor for class org.intermine.web.struts.SharingBagUsersController
-
- SharingInvite - Class in org.intermine.api.bag
-
A representation of an invitation to share a resource.
- SharingInvite(InterMineBag, String) - Constructor for class org.intermine.api.bag.SharingInvite
-
Constructor.
- SharingInvite(InterMineBag, String, String) - Constructor for class org.intermine.api.bag.SharingInvite
-
Constructor.
- SharingInvite(InterMineBag, String, String, Date, Date, Boolean) - Constructor for class org.intermine.api.bag.SharingInvite
-
Constructor.
- SharingInvite.IntermediateRepresentation - Class in org.intermine.api.bag
-
A structure for holding data we read from the DB.
- SharingInvite.IntermediateRepresentation() - Constructor for class org.intermine.api.bag.SharingInvite.IntermediateRepresentation
-
- SharingInvite.NotFoundException - Exception in org.intermine.api.bag
-
Exception thrown when we can't find a shared invitation.
- shortName - Variable in class org.intermine.bio.dataconversion.BioGridConverter.ExperimentHolder
-
- shouldCancelQuery() - Method in interface org.intermine.web.logic.query.QueryMonitor
-
Called intermittently while a query is run providing an opportunity to cancel
the query.
- shouldCancelQuery() - Method in class org.intermine.web.logic.query.QueryMonitorTimeout
-
Return true if tickle has not been called in a period of time greater than the
timeout value.
- shouldSavePopulation() - Method in class org.intermine.webservice.server.widget.WidgetsServiceInput
-
- showColumn(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
-
Deprecated.
as we don't hide columns any more
- shuffle(Map<String, V>, int) - Static method in class org.intermine.web.logic.WebUtil
-
takes a map and puts it in random order also shortens the list to be
map.size() = max
- shutdown() - Method in class org.intermine.api.tracker.TrackerDelegate
-
Called from ShutdownHook.
- shutdown() - Method in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
Called by the ShutdownHook on shutdown.
- shutdown() - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Called by the StatsShutdownHook on shutdown
- shutdown() - Method in class org.intermine.sql.Database
-
Logs stuff
- shutdown() - Method in interface org.intermine.util.Shutdownable
-
Shuts down an instance.
- shutdown() - Static method in class org.intermine.util.ShutdownHook
-
Performs the shutdown.
- shutdown() - Method in class org.intermine.web.context.InterMineContext
-
Send the signal that shutdown is happening - try and release resources.
- Shutdownable - Interface in org.intermine.util
-
An interface for any object that can be shut down by the ShutdownHook.
- ShutdownHook - Class in org.intermine.util
-
This class provides a "shutdown" service to other classes.
- SimpleConstraint - Class in org.intermine.objectstore.query
-
Represents a constraint between two QueryEvaluable types.
- SimpleConstraint(QueryEvaluable, ConstraintOp, QueryEvaluable) - Constructor for class org.intermine.objectstore.query.SimpleConstraint
-
Construct a Constraint.
- SimpleConstraint(QueryEvaluable, ConstraintOp) - Constructor for class org.intermine.objectstore.query.SimpleConstraint
-
Construct a Constraint.
- simpleConstraintToString(SqlGenerator.State, StringBuffer, SimpleConstraint, Query) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Converts a SimpleConstraint object into a String suitable for putting in an SQL query.
- simpleCreateObject(Class<C>) - Static method in class org.intermine.util.DynamicUtil
-
Create a new object given a class, which may be an interface.
- SingleTemplateService - Class in org.intermine.webservice.server.template
-
Service that responds with a single template.
- SingleTemplateService(InterMineAPI) - Constructor for class org.intermine.webservice.server.template.SingleTemplateService
-
- SINGLETON - Static variable in class org.intermine.util.NullFirstComparator
-
Publicly-accessible instance
- SingletonResults - Class in org.intermine.objectstore.query
-
This class is equivalent to a Result object with ResultRows consisting only of single items
- SingletonResults(Query, ObjectStore, Map<Object, Integer>) - Constructor for class org.intermine.objectstore.query.SingletonResults
-
Constructor for a SingletonResults object
- SingletonResults(ResultsBatches, boolean, boolean, boolean) - Constructor for class org.intermine.objectstore.query.SingletonResults
-
Constructor for a SingletonResults object, given a ResultsBatches object.
- singletonResultsCache - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- size() - Method in class org.intermine.api.profile.StorableBag
-
Returns the number of elements in the bag.
- size() - Method in class org.intermine.api.results.flatouterjoins.ResultsFlatOuterJoinsImpl
- size() - Method in class org.intermine.api.results.WebResults
- size() - Method in class org.intermine.api.search.SearchResults
-
- size() - Method in class org.intermine.objectstore.proxy.ProxyCollection
-
Gets the number of elements in this collection
- size() - Method in class org.intermine.objectstore.query.Results
-
Gets the number of results rows in this Results object
- size(boolean, boolean) - Method in class org.intermine.objectstore.query.ResultsBatches
-
Gets the number of results rows in this Results object.
- SIZE - Static variable in class org.intermine.objectstore.query.ResultsInfo
-
Denotes that the result of getRows() is the known size of the results.
- size() - Method in class org.intermine.util.AlwaysMap
- size() - Method in class org.intermine.util.ConsistentSet
-
Return the number of elements in this Set.
- size() - Method in class org.intermine.util.IdentityMap
- size() - Method in class org.intermine.util.IntPresentSet
-
Returns the number of ints present.
- size() - Method in class org.intermine.util.IntToIntMap
-
Returns the number of mappings to non-minus-one ints present.
- size() - Method in class org.intermine.util.PseudoSet
- size() - Method in class org.intermine.util.ReferenceMap
- size - Variable in class org.intermine.web.logic.results.InlineResultsTable
-
- size() - Method in class org.intermine.webservice.client.lists.ItemList
-
Synonym for getSize()
- size() - Method in class org.intermine.webservice.client.results.JsonRow
-
- size() - Method in class org.intermine.webservice.client.results.ResultRowList
-
- sizeOfArray(Object[]) - Static method in class org.intermine.sql.writebatch.TableBatch
-
Calculates the size of an array, in bytes.
- sizeOfList(List<Object[]>) - Static method in class org.intermine.sql.writebatch.TableBatch
-
Calculates the size of a List of arrays, in bytes.
- SKELETON - Static variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
- skeletons - Variable in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
-
- SKIP_BUILDER_PARAMETER - Static variable in class org.intermine.web.struts.TemplateAction
-
Name of skipBuilder parameter
- SOClassNameMapMakerTask - Class in org.intermine.bio.task
-
A Task that reads a SO OBO files and writes a file mapping SO term names to FlyMine class names.
- SOClassNameMapMakerTask() - Constructor for class org.intermine.bio.task.SOClassNameMapMakerTask
-
Create a new SOClassNameMapMakerTask object.
- SoftReferenceMap<K,V> - Class in org.intermine.util
-
This is a Map implementation designed specifically for people intending to create a cache.
- SoftReferenceMap() - Constructor for class org.intermine.util.SoftReferenceMap
-
- SortableMap<K extends java.lang.Comparable<K>,V extends java.lang.Comparable<V>> - Class in org.intermine.web.logic
-
SortableMap extends a LinkedHashMap with some useful sorting features.
- SortableMap() - Constructor for class org.intermine.web.logic.SortableMap
-
Default constructor.
- SortableMap(Map<K, V>) - Constructor for class org.intermine.web.logic.SortableMap
-
Create new SortableMap based on the given Map.
- sortConstraints(List<PathConstraint>) - Method in class org.intermine.pathquery.PathQuery
-
A method to sort constraints by a given lists, provided to allow TemplateQuery to set a
specific sort order that will be preserved in a round-trip to XML.
- sortKeys() - Method in class org.intermine.web.logic.SortableMap
-
Sort this map ascending on keys in natural order (default).
- sortKeys(boolean, boolean) - Method in class org.intermine.web.logic.SortableMap
-
Sort this map on keys.
- sortMap(Map<String, BigDecimal>) - Static method in class org.intermine.web.logic.widget.ErrorCorrection
-
Sort the map by values.
- sortValues() - Method in class org.intermine.web.logic.SortableMap
-
Sort this map ascending on values in natural order (default).
- sortValues(boolean, boolean) - Method in class org.intermine.web.logic.SortableMap
-
Sort this map on values.
- SOToModelTask - Class in org.intermine.bio.task
-
A Task that reads a SO OBO files and writes so_additions.xml
- SOToModelTask() - Constructor for class org.intermine.bio.task.SOToModelTask
-
- source - Variable in class org.intermine.dataloader.BatchingFetcher
-
- SOURCE - Static variable in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
- source - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
-
- Source - Class in org.intermine.dataloader
-
Represents a data source, by name and skeleton status.
- Source(String, String, boolean) - Constructor for class org.intermine.dataloader.Source
-
Create a new source object.
- Source(String, String) - Constructor for class org.intermine.dataloader.Source
-
Create a new source object that isn't a skeleton.
- Source(String, boolean) - Constructor for class org.intermine.dataloader.Source
-
Create a new source object with no type information.
- Source(String) - Constructor for class org.intermine.dataloader.Source
-
Create a new source object with no type information that isn't a skeleton
- sourceKeys - Static variable in class org.intermine.dataloader.DataLoaderHelper
-
- sourceName - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
-
- sourceName - Variable in class org.intermine.dataloader.XmlDataLoaderTask
-
- sourceName - Variable in class org.intermine.task.DirectDataLoaderTask
-
- sourceName - Variable in class org.intermine.task.FullXmlConverterTask
-
- SourcePriorityComparator - Class in org.intermine.dataloader
-
Comparator, that compares two InterMineObjects, with reference to a particular
FieldDescriptor for priority.
- SourcePriorityComparator(DataTracker, Class<? extends InterMineObject>, String, Source, InterMineObject, IntPresentSet, IntegrationWriterAbstractImpl, Source, Source, PriorityConfig) - Constructor for class org.intermine.dataloader.SourcePriorityComparator
-
Constructs a new Comparator for comparing objects for priority for a given field.
- sourceToString(Source) - Method in class org.intermine.dataloader.DataTracker
-
Converts a Source to a source name.
- sourceType - Variable in class org.intermine.dataloader.ObjectStoreDataLoaderTask
-
- SPACE - Static variable in class org.intermine.api.query.codegen.WebserviceJavaCodeGenerator
-
- SPACE - Static variable in class org.intermine.api.query.codegen.WebservicePerlCodeGenerator
-
- SPACE - Static variable in class org.intermine.api.query.codegen.WebservicePythonCodeGenerator
-
- SPACE - Static variable in class org.intermine.api.query.codegen.WebserviceRubyCodeGenerator
-
- SPACE_SPLITTER - Static variable in class org.intermine.pathquery.PathQuery
-
A Pattern that finds spaces in a String.
- split(List<? extends Collection<String>>) - Method in class org.intermine.pathquery.LogicExpression
-
Takes a List of collections of String variables and returns a List of the same length,
containing sections of the LogicExpression with those variables in.
- SPLITTER - Static variable in class org.intermine.objectstore.intermine.NotXmlParser
-
A Pattern that will find delimiters.
- sqlCache - Static variable in class org.intermine.objectstore.intermine.SqlGenerator
-
- SqlGenerator - Class in org.intermine.objectstore.intermine
-
Code to generate an sql statement from a Query object.
- SqlGenerator.State - Class in org.intermine.objectstore.intermine
-
Internal representation of the State of the query as it is built up.
- SqlGenerator.State() - Constructor for class org.intermine.objectstore.intermine.SqlGenerator.State
-
Constructor
- SQLOperation<T> - Class in org.intermine.objectstore.intermine
-
A functional interface (oh, please come Java 8 - you cannot come soon
enough) to help manage out-of-control boilerplate-itis in SQL code.
- SQLOperation() - Constructor for class org.intermine.objectstore.intermine.SQLOperation
-
- SQLStringable - Interface in org.intermine.sql.query
-
An interface for all classes that implement the getSQLString method.
- StandardHttpExporter - Class in org.intermine.web.logic.export.http
-
Abstract class implementing functionality common for exporters exporting table in simple format
like comma separated format.
- StandardHttpExporter() - Constructor for class org.intermine.web.logic.export.http.StandardHttpExporter
-
Constructor.
- start - Variable in class org.intermine.dataconversion.FullXmlConverter
-
- start - Variable in class org.intermine.objectstore.query.OverlapRange
-
- start - Variable in class org.intermine.objectstore.query.ResultsInfo
-
- start - Variable in class org.intermine.sql.precompute.BestQueryExplainer
-
- start - Variable in class org.intermine.sql.query.ExplainResult
-
- START_PARAMETER - Static variable in class org.intermine.webservice.server.WebServiceRequestParser
-
Name of start parameter that determines index of first returned result.
- START_PATHS - Static variable in class org.intermine.web.struts.InterMineRequestProcessor
-
Paths that can be used as initial pages ie. when there is no session.
- startClass - Variable in class org.intermine.web.logic.widget.WidgetLdr
-
- startContainsClass(String) - Method in class org.intermine.pathquery.Path
-
Return true if the first element in the path has the class given in input as type
- startDocument() - Method in class org.intermine.webservice.server.ServiceListingHandler
-
- startElement(String, String, String, Attributes) - Method in class org.intermine.api.bag.BagQueryHandler
- startElement(String, String, String, Attributes) - Method in class org.intermine.api.bag.InvitationHandler
- startElement(String, String, String, Attributes) - Method in class org.intermine.api.profile.PreferencesHandler
- startElement(String, String, String, Attributes) - Method in class org.intermine.api.profile.TagHandler
- startElement(String, String, String, Attributes) - Method in class org.intermine.api.tracker.xml.TrackManagerHandler
- startElement(String, String, String, Attributes) - Method in class org.intermine.api.xml.InterMineBagHandler
-
InvalidBag
- startElement(String, String, String, Attributes) - Method in class org.intermine.api.xml.SavedQueryHandler
- startElement(String, String, String, Attributes) - Method in class org.intermine.api.xml.SharedBagHandler
- startElement(String, String, String, Attributes) - Method in class org.intermine.pathquery.PathQueryHandler
- startElement(String, String, String, Attributes) - Method in class org.intermine.template.xml.TemplateQueryHandler
- startElement(String, String, String, Attributes) - Method in class org.intermine.webservice.server.ServiceListingHandler
-
- startElement(String, String, String, Attributes) - Method in class org.intermine.xml.full.FullHandler
- startListening() - Method in class org.intermine.api.search.SearchRepository
-
Begin listening for events on the items of interest.
- startPagedTableCount(PageTableQueryMonitor, HttpSession, MessageResources) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Start a query running in the background that will return the row count of the collection.
- startQuery(QueryMonitor, HttpSession, MessageResources, boolean, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Start the current query running in the background, then return.
- startQueryCount(QueryCountQueryMonitor, HttpSession, MessageResources) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Start a query running in the background that will return the row count of the query argument.
- startQueryWithTimeout(HttpServletRequest, boolean, PathQuery) - Static method in class org.intermine.web.logic.session.SessionMethods
-
Start the given query running in the background, then return, with a default timeout.
- startTemplateBuild(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
-
Put query builder in template building mode.
- StaticMethodTask - Class in org.intermine.task
-
Given a class name and method name, just invokes a static method.
- StaticMethodTask() - Constructor for class org.intermine.task.StaticMethodTask
-
- stats - Variable in class org.intermine.sql.writebatch.BatchWriterSimpleImpl
-
- statsBagTableTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- statsConTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- statsEstTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- statsExeTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- statsGenTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- statsOptTime - Variable in class org.intermine.objectstore.intermine.ObjectStoreInterMineImpl
-
- StatusDictionary - Class in org.intermine.webservice.server
-
HTTP status code dictionary.
- STDDEV - Static variable in class org.intermine.objectstore.query.QueryFunction
-
Sample standard deviation of a number of rows
- STDDEV - Static variable in class org.intermine.sql.query.Function
-
STDDEV operator - takes one operand
- stm - Variable in class org.intermine.api.tracker.xml.TrackHandler
-
- StockProcessor - Class in org.intermine.bio.dataconversion
-
A ChadoProcessor for the chado stock module.
- StockProcessor(ChadoDBConverter) - Constructor for class org.intermine.bio.dataconversion.StockProcessor
-
Create a new ChadoProcessor
- stop() - Method in class org.intermine.webservice.server.idresolution.JobJanitor
-
Let others tell us to stop.
- stopListening() - Method in class org.intermine.api.search.SearchRepository
-
Stop listening for events
- stopTemplateBuild(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.QueryBuilderChange
-
Bring the query builder out of template building mode and discard any unfinished template
building.
- StorableBag - Class in org.intermine.api.profile
-
Base class for representations of user's collections of objects stored in a database.
- StorableBag() - Constructor for class org.intermine.api.profile.StorableBag
-
- store(Connection) - Method in interface org.intermine.api.tracker.track.Track
-
Save into the table the track object representing the user activity
- store(Connection) - Method in class org.intermine.api.tracker.track.TrackAbstract
-
- store(Item, int) - Method in class org.intermine.bio.dataconversion.FlyBaseProcessor
-
Store the feature Item.
- store(Item, int) - Method in class org.intermine.bio.dataconversion.SequenceProcessor
-
Store the feature Item.
- store(Item, int) - Method in class org.intermine.bio.dataconversion.WormBaseProcessor
-
Store the feature Item.
- store(Item) - Method in class org.intermine.dataconversion.DataConverter
-
Store a single XML Item
- store(ReferenceList, Integer) - Method in class org.intermine.dataconversion.DataConverter
-
Store a single XML ReferenceList
- store(Attribute, Integer) - Method in class org.intermine.dataconversion.DataConverter
-
Store a single XML Attribute
- store(Reference, Integer) - Method in class org.intermine.dataconversion.DataConverter
-
Store a single XML Reference
- store(Collection<Item>) - Method in class org.intermine.dataconversion.DataConverter
-
Store a Collection of XMl Items
- store(Item) - Method in interface org.intermine.dataconversion.ItemWriter
-
Stores the given Item and all its associated attributes, references, and referencelists.
- store(ReferenceList, Integer) - Method in interface org.intermine.dataconversion.ItemWriter
-
Stores the given ReferenceList after setting its item id.
- store(Reference, Integer) - Method in interface org.intermine.dataconversion.ItemWriter
-
Stores the given Reference after setting its item id.
- store(Attribute, Integer) - Method in interface org.intermine.dataconversion.ItemWriter
-
Stores the given Attribute after setting its item id.
- store(Item) - Method in class org.intermine.dataconversion.MockItemWriter
-
Stores the given Item and all its associated attributes, references, and referencelists.
- store(ReferenceList, Integer) - Method in class org.intermine.dataconversion.MockItemWriter
-
Stores the given ReferenceList after setting its item id.
- store(Reference, Integer) - Method in class org.intermine.dataconversion.MockItemWriter
-
Stores the given Reference after setting its item id.
- store(Attribute, Integer) - Method in class org.intermine.dataconversion.MockItemWriter
-
Stores the given Attribute after setting its item id.
- store(Item) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
-
Stores the given Item and all its associated attributes, references, and referencelists.
- store(ReferenceList, Integer) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
-
Stores the given ReferenceList after setting its item id.
- store(Reference, Integer) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
-
Stores the given Reference after setting its item id.
- store(Attribute, Integer) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
-
Stores the given Attribute after setting its item id.
- store(FastPathObject) - Method in class org.intermine.dataloader.DirectDataLoader
-
Store an object using the IntegrationWriter, buffering writes so that integration queries
and database writes can be run in batches.
- store(FastPathObject, Source, Source) - Method in interface org.intermine.dataloader.IntegrationWriter
-
Stores the given object in the objectstore.
- store(FastPathObject, Source, Source) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Stores the given object in the objectstore.
- store(FastPathObject, Source, Source, int) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Stores the given object in the objectstore.
- store(Object) - Method in class org.intermine.dataloader.IntegrationWriterAbstractImpl
-
Store an object in this ObjectStore, delegates to internal ObjectStoreWriter.
- store(FastPathObject, Source, Source, int) - Method in class org.intermine.dataloader.IntegrationWriterDataTrackingImpl
-
Stores the given object in the objectstore.
- store(Database, String, String) - Static method in class org.intermine.modelproduction.MetadataManager
-
Store a (key, value) pair in the metadata table of the database
- store(Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Store an object in this ObjectStore.
- store(Object) - Method in interface org.intermine.objectstore.ObjectStoreWriter
-
Store an object in this ObjectStore.
- storeAll() - Method in class org.intermine.bio.dataconversion.GFF3Converter
-
store all the items
- storeAll(Collection<Item>) - Method in interface org.intermine.dataconversion.ItemWriter
-
Stores the given Collection of Items and all their associated attributes, references, and
referencelists.
- storeAll(Collection<Item>) - Method in class org.intermine.dataconversion.MockItemWriter
-
Stores the given Collection of Items and all their associated attributes, references, and
referencelists.
- storeAll(Collection<Item>) - Method in class org.intermine.dataconversion.ObjectStoreItemWriter
-
Stores the given Collection of Items and all their associated attributes, references, and
referencelists.
- storeBinary(Database, String, byte[]) - Static method in class org.intermine.modelproduction.MetadataManager
-
Store a binary (key, value) pair in the metadata table of the database
- storeException(HttpServletRequest, String, ActionMessage, ActionForward, String) - Method in class org.intermine.web.struts.InterMineExceptionHandler
-
Default implementation for handling an ActionMessage generated
from an Exception during Action delegation.
- storeInvites(Profile) - Method in class org.intermine.api.bag.InvitationHandler
-
- storeItems() - Method in class org.intermine.bio.dataconversion.OboConverter
-
Convert DagTerms into Items and relation Items, and write them to the ItemWriter
- storeLargeBinary(Database, String) - Static method in class org.intermine.modelproduction.MetadataManager
-
Returns an OutputStream object with which to write a large binary value to the database.
- StoreMetadataTask - Class in org.intermine.task
-
Store model metadata to a database
- StoreMetadataTask() - Constructor for class org.intermine.task.StoreMetadataTask
-
- storeSavedBag() - Method in class org.intermine.api.profile.StorableBag
-
Perform the actual insertion of data into the userprofile database.
- storeTrack(Track) - Method in class org.intermine.api.tracker.AbstractTracker
-
Save into the table the track object representing the user activity
- storeTrack(Track) - Method in interface org.intermine.api.tracker.Tracker
-
Save into the table a Track
- storeWithConnection(Connection, Object) - Method in class org.intermine.objectstore.intermine.ObjectStoreWriterInterMineImpl
-
Performs store with a given Connection.
- StreamedOutput - Class in org.intermine.webservice.server.output
-
Immediately as the data or error messages are added they are streamed via http connection.
- StreamedOutput(PrintWriter, Formatter) - Constructor for class org.intermine.webservice.server.output.StreamedOutput
-
Constructor.
- StreamedOutput(PrintWriter, Formatter, String) - Constructor for class org.intermine.webservice.server.output.StreamedOutput
-
Constructor.
- STRING_OPS - Static variable in class org.intermine.objectstore.query.SimpleConstraint
-
- StringHelper - Class in org.intermine.api.query.range
-
- StringHelper() - Constructor for class org.intermine.api.query.range.StringHelper
-
- StringTableExporter - Class in org.intermine.web.logic.export.string
-
Simple exporter exporting table of strings.
- StringTableExporter(PrintWriter, RowFormatter) - Constructor for class org.intermine.web.logic.export.string.StringTableExporter
-
Constructor.
- stringToSource(String) - Method in class org.intermine.dataloader.DataTracker
-
Converts a string sourcename to a Source.
- stringToSource(String, String) - Method in class org.intermine.dataloader.DataTracker
-
Converts a string sourcename to a Source if the type is known.
- stripStart(String, Properties) - Static method in class org.intermine.util.PropertiesUtil
-
Strips the given string off the keys of the given
Properties, and returns a new set of properties.
- STRPOS - Static variable in class org.intermine.sql.query.Function
-
STRPOS operator - takes two operands.
- SUB - Static variable in class org.intermine.web.logic.config.HeaderConfigTitle
-
A subtitle.
- SUBCLASSES - Static variable in class org.intermine.web.logic.Constants
-
ServletContext attribute, Map from unqualified type name to list of subclass names.
- subclassValue - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
-
- subIter - Variable in class org.intermine.api.results.ExportResultsIterator
-
- subList(int, int) - Method in class org.intermine.objectstore.query.Results
- subList(int, int) - Method in class org.intermine.webservice.client.results.ResultRowList
-
- subMap - Variable in class org.intermine.util.ReferenceMap
-
- SubMenuController - Class in org.intermine.web.struts
-
Controller for the submenu at the top of every page
- SubMenuController() - Constructor for class org.intermine.web.struts.SubMenuController
-
- submit(BagQueryRunner, JobInput) - Method in class org.intermine.api.idresolution.IDResolver
-
- submit(BagQueryUpgrade) - Method in class org.intermine.api.idresolution.IDResolver
-
- subquery - Variable in class org.intermine.objectstore.query.SubqueryConstraint
-
- subquery - Variable in class org.intermine.objectstore.query.SubqueryExistsConstraint
-
- SubQuery - Class in org.intermine.sql.query
-
A representation of a subquery that can be present in the FROM section of an SQL query.
- SubQuery(Query, String) - Constructor for class org.intermine.sql.query.SubQuery
-
Constructor for this SubQuery object.
- SubqueryConstraint - Class in org.intermine.objectstore.query
-
Constrain a QueryClass or QueryEvaluable to be within the select list
of a given subquery.
- SubqueryConstraint(QueryEvaluable, ConstraintOp, Query) - Constructor for class org.intermine.objectstore.query.SubqueryConstraint
-
Construct a SubqueryConstraint with a QueryEvaluable
- SubqueryConstraint(QueryClass, ConstraintOp, Query) - Constructor for class org.intermine.objectstore.query.SubqueryConstraint
-
Construct a SubqueryConstraint with a QueryClass
- SubQueryConstraint - Class in org.intermine.sql.query
-
A representation of a constraint where an AbstractValue is IN the results of a Query.
- SubQueryConstraint(AbstractValue, Query) - Constructor for class org.intermine.sql.query.SubQueryConstraint
-
Constructor for SubQueryConstraint object.
- subqueryConstraintToString(SqlGenerator.State, StringBuffer, SubqueryConstraint, Query, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Converts a SubqueryConstraint object into a String suitable for putting in an SQL query.
- SubqueryExistsConstraint - Class in org.intermine.objectstore.query
-
Check if there are any rows in the subquery
- SubqueryExistsConstraint(ConstraintOp, Query) - Constructor for class org.intermine.objectstore.query.SubqueryExistsConstraint
-
Construct a SubqueryExistsConstraint
- subqueryExistsConstraintToString(SqlGenerator.State, StringBuffer, SubqueryExistsConstraint, DatabaseSchema) - Static method in class org.intermine.objectstore.intermine.SqlGenerator
-
Converts a SubqueryExistsConstraint object into a String suitable for putting in an SQL
query.
- subscribe(String, Properties) - Static method in class org.intermine.util.MailUtils
-
Subscribe the given email address to the mailing list specified in the
mine config file
- subscribeToList(String) - Method in class org.intermine.util.Emailer
-
Subscribe a user to a mailing list.
- subscribeToList(String) - Method in class org.intermine.web.context.NullMailer
-
- subSequence(int, int) - Method in class org.intermine.bio.util.ClobAccessReverseComplement
-
Returns a new CharSequence that is a subsequence of this sequence, from start (inclusive) to
end (exclusive).
- subSequence - Variable in class org.intermine.objectstore.query.ClobAccess
-
- subSequence(int, int) - Method in class org.intermine.objectstore.query.ClobAccess
-
Returns a new CharSequence that is a subsequence of this sequence, from start (inclusive) to
end (exclusive).
- subSequence(int, int) - Method in class org.intermine.objectstore.query.PendingClob
-
Returns a new CharSequence that is a subsequence of this sequence, from start (inclusive) to
end (exclusive).
- SUBSTR - Static variable in class org.intermine.sql.query.Function
-
SUBSTR operator - takes two or three operands.
- SUBSTRING - Static variable in class org.intermine.objectstore.query.QueryExpression
-
Substring of specified length from index in string
- SubTable - Class in org.intermine.webservice.server.core
-
A class that represents a table nested within a cell in another table.
- SubTable(Path, List<Path>, List<List<Either<ResultCell, SubTable>>>) - Constructor for class org.intermine.webservice.server.core.SubTable
-
Construct a sub table.
- subtabs - Variable in class org.intermine.web.logic.results.WebState
-
- SUBTRACT - Static variable in class org.intermine.api.bag.BagOperations
-
Constant representing logical substraction.
- subtract(Model, Collection<InterMineBag>, String, Profile, ClassKeys) - Static method in class org.intermine.api.bag.BagOperations
-
Create a bag that contains the union of the bags provided minus the intersection of those
bags.
- SUBTRACT - Static variable in class org.intermine.objectstore.query.QueryExpression
-
Subtraction of two numeric fields
- subtract(ItemList...) - Method in class org.intermine.webservice.client.lists.ItemList
-
Remove the items in the given lists from this list.
- subtract(ListService.ListOperationInfo, ItemList...) - Method in class org.intermine.webservice.client.lists.ItemList
-
Remove the items in the given lists from this list.
- subtract(Collection<ItemList>) - Method in class org.intermine.webservice.client.lists.ItemList
-
Remove the items in the given lists from this list.
- subtract(ListService.ListOperationInfo, Collection<ItemList>) - Method in class org.intermine.webservice.client.lists.ItemList
-
Remove the items in the given lists from this list.
- subtract(ListService.ListOperationInfo, ItemList, ItemList...) - Method in class org.intermine.webservice.client.services.ListService
-
Subtract some lists from some other lists to produce a new list.
- subtract(ListService.ListOperationInfo, ItemList[], ItemList...) - Method in class org.intermine.webservice.client.services.ListService
-
Subtract some lists from some other lists to produce a new list.
- subtract(ItemList, ItemList...) - Method in class org.intermine.webservice.client.services.ListService
-
Subtract some lists from some other lists to produce a new list.
- subtract(ItemList[], ItemList...) - Method in class org.intermine.webservice.client.services.ListService
-
Subtract some lists from some other lists to produce a new list.
- subtract(Collection<ItemList>, Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService
-
Subtract some lists from some other lists to produce a new list.
- subtract(ListService.ListOperationInfo, Collection<ItemList>, Collection<ItemList>) - Method in class org.intermine.webservice.client.services.ListService
-
Subtract some lists from some other lists to produce a new list.
- SUBTRACT_PARAM - Static variable in class org.intermine.webservice.server.lists.ListInput
-
Things to subtract
- SUM - Static variable in class org.intermine.objectstore.query.QueryFunction
-
Sum of a number of rows
- SUM - Static variable in class org.intermine.sql.query.Function
-
SUM(v) aggregate function - takes one operand.
- summarise(ApiTemplate) - Method in class org.intermine.api.template.TemplateSummariser
-
Populates the possibleValues data for a given TemplateQuery from the os.
- summarise(String) - Method in class org.intermine.dwr.AjaxServices
-
Summarises the given template query.
- summariseAsOccurrences(String) - Static method in class org.intermine.api.query.MainHelper.SummaryConfig
-
Returns whether the given field name is configured to be summarised as a count of
occurrences.
- SummariseObjectStoreTask - Class in org.intermine.task
-
Summarise an ObjectStore into a particular properties file.
- SummariseObjectStoreTask() - Constructor for class org.intermine.task.SummariseObjectStoreTask
-
- summariseQuery(PathQuery, String, boolean) - Method in class org.intermine.api.query.QueryExecutor
-
Returns the results for a summary for a column in a PathQuery.
- summariseQuery(PathQuery, String) - Method in class org.intermine.api.query.QueryExecutor
-
- summariseQuery(PathQuery, String, String, boolean) - Method in class org.intermine.api.query.QueryExecutor
-
Summarise a query.
- SummariseTemplatesAction - Class in org.intermine.web.struts
-
Action to summarise all templates.
- SummariseTemplatesAction() - Constructor for class org.intermine.web.struts.SummariseTemplatesAction
-
- summaryBatchSize - Variable in class org.intermine.api.query.QueryExecutor
-
- summaryCallCounts - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
-
- SummaryConstraint - Class in org.intermine.web.logic.querybuilder
-
Representation of a PathQuery constraint with additional information for display in the
QueryBuilder summary section.
- SummaryConstraint(PathConstraint, String, boolean, String, String) - Constructor for class org.intermine.web.logic.querybuilder.SummaryConstraint
-
Construct with the underlying PathConstraint and additional details from the PathQuery.
- summaryCounts - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
-
- SummaryPath - Class in org.intermine.web.logic.querybuilder
-
Representation of a query path with additional information for display in the QueryBulder summary
section.
- SummaryPath(Path, boolean, boolean) - Constructor for class org.intermine.web.logic.querybuilder.SummaryPath
-
Construct a summary path with details of whether the path is locked and/or forced to be an
inner join.
- SummaryService - Class in org.intermine.webservice.server
-
Serve up the paths used to summarise each class.
- SummaryService(InterMineAPI) - Constructor for class org.intermine.webservice.server.SummaryService
-
Constructor
- SummaryServlet - Class in org.intermine.webservice.server
-
Returns a summary field information.
- SummaryServlet() - Constructor for class org.intermine.webservice.server.SummaryServlet
-
- summaryTimes - Variable in class org.intermine.dataloader.BaseEquivalentObjectFetcher
-
- superUsers - Variable in class org.intermine.web.struts.ModifySuperUserForm
-
- swapColumns(int, int) - Method in class org.intermine.web.logic.results.PagedTable
-
Deprecated.
Swap 2 columns
- swapColumns(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class org.intermine.web.struts.ChangeTableAction
-
Deprecated.
as we don't move columns any more
- switchable - Variable in class org.intermine.web.struts.QueryBuilderConstraintForm
-
- SwitchOffAbility - Enum in org.intermine.template
-
Enumeration for describing the configuration on constraints on a TemplateQuery that determines
whether a user is allowed to switch off a constraint, and if so what state it is in.
- SymmetricDifference - Class in org.intermine.api.bag.operations
-
- SymmetricDifference(Model, Profile, Collection<InterMineBag>) - Constructor for class org.intermine.api.bag.operations.SymmetricDifference
-
- SynchronisedIterator<E> - Class in org.intermine.util
-
An Iterator that passes through to an underlying Iterator, synchronising all calls.
- SynchronisedIterator(Iterator<E>) - Constructor for class org.intermine.util.SynchronisedIterator
-
Constructs a SynchronisedIterator from an Iterator.
- synchroniseWithDatabase(Connection) - Method in class org.intermine.sql.precompute.PrecomputedTableManager
-
Synchronise with the underlying database
- synonyms - Variable in class org.intermine.bio.dataconversion.GeneInfoRecord
-
- synonyms - Variable in class org.intermine.bio.dataconversion.GFF3RecordHandler
-
- synToItem - Variable in class org.intermine.bio.dataconversion.OboConverter
-